Tear lipocalin muteins binding il-4 r alpha

ABSTRACT

The present invention relates to novel muteins derived from human tear lipocalin, which bind to IL 4 receptor alpha. The sequences of the muteins comprise particular combinations of amino acids. In particular a mutated amino acid residue is present at any one or more of the sequence positions 27, 28 30, 31, 33, 53, 57, 61, 64, 66, 80, 83, 104-106 and 108 of the linear polypeptide sequence of the mature human tear lipocalin. A mutated amino acid residue is also present at any 2 or more of the sequence positions 26, 32, 34, 55, 56, 58 and 63 of the linear polypeptide sequence of the mature human tear lipocalin. The invention also provides a corresponding nucleic acid molecule encoding such a mutein and a method for producing such a mutein and its encoding nucleic acid molecule.

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

This application is a Continuation of U.S. application Ser. No.14/665,692, filed Mar. 23, 2015, incorporated herein by reference in itsentirety, which is a Continuation of U.S. application Ser. No.13/702,792 (National Stage of PCT/EP2011/059420), filed Dec. 7, 2012,incorporated herein by reference in its entirety, which claims priorityfrom Provisional Application U.S. Application 61/352,461, filed Jun. 8,2010, incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to muteins of human tear lipocalin thatbind to IL-4 receptor alpha. The invention also relates to correspondingnucleic acid molecules encoding such a mutein and to a method for theirgeneration. The invention further relates a method for producing such amutein. Finally, the invention is directed to a pharmaceuticalcomposition that includes such a lipocalin mutein as well as to varioususes of the mutein.

BACKGROUND

Proteins that selectively bind to selected targets by way ofnon-covalent interaction play a crucial role as reagents inbiotechnology, medicine, bioanalytics as well as in the biological andlife sciences in general. Antibodies, i.e. immunoglobulins, are aprominent example of this class of proteins. Despite the manifold needsfor such proteins in conjunction with recognition, binding and/orseparation of ligands/targets, almost exclusively immunoglobulins arecurrently used. The application of other proteins with definedligand-binding characteristics, for example the lectins, has remainedrestricted to special cases.

Additional proteinaceous binding molecules that have antibody-likefunctions are the members of the lipocalin family, which have naturallyevolved to bind ligands. Lipocalins occur in many organisms, includingvertebrates, insects, plants and bacteria. The members of the lipocalinprotein family (Pervaiz, S., & Brew, K. (1987) FASEB J. 1, 209-214) aretypically small, secreted proteins and have a single polypeptide chain.They are characterized by a range of different molecular-recognitionproperties: their ability to bind various, principally hydrophobicmolecules (such as retinoids, fatty acids, cholesterols, prostaglandins,biliverdins, pheromones, tastants, and odorants), their binding tospecific cell-surface receptors and their formation of macromolecularcomplexes. Although they have, in the past, been classified primarily astransport proteins, it is now clear that the lipocalins fulfill avariety of physiological functions. These include roles in retinoltransport, olfaction, pheromone signaling, and the synthesis ofprostaglandins. The lipocalins have also been implicated in theregulation of the immune response and the mediation of cell homoeostasis(reviewed, for example, in Flower, D. R. (1996) Biochem. J. 318, 1-14and Flower, D. R. et al. (2000) Biochim. Biophys. Acta 1482, 9-24).

The lipocalins share unusually low levels of overall sequenceconservation, often with sequence identities of less than 20%. In strongcontrast, their overall folding pattern is highly conserved. The centralpart of the lipocalin structure consists of a single eight-strandedanti-parallel β-sheet closed back on itself to form a continuouslyhydrogen-bonded β-barrel. This β-barrel forms a central cavity. One endof the barrel is sterically blocked by the N-terminal peptide segmentthat runs across its bottom as well as three peptide loops connectingthe β-strands. The other end of the β-barrel is open to the solvent andencompasses a target-binding site, which is formed by four flexiblepeptide loops. It is this diversity of the loops in the otherwise rigidlipocalin scaffold that gives rise to a variety of different bindingmodes each capable of accommodating targets of different size, shape,and chemical character (reviewed, e.g., in Flower, D. R. (1996), supra;Flower, D. R. et al. (2000), supra, or Skerra, A. (2000) Biochim.Biophys. Acta 1482, 337-350).

International patent application WO 99/16873 discloses polypeptides ofthe lipocalin family with mutated amino acid positions in the region ofthe four peptide loops, which are arranged at the end of the cylindricalβ-barrel structure encompassing the binding pocket, and which correspondto those segments in the linear polypeptide sequence that includes theamino acid positions 28 to 45, 58 to 69, 86 to 99, and 114 to 129 of thebilin-binding protein of Pieris brassicae. Members of the lipocalinfamily have been reported to be post-translationally modified, e.g.phosphorylation and glycosylation of tear lipocalin (e.g. You, J., etal. (2010) Electrophoresis 31, 1853-1861). Nevertheless nopost-translational modification is required for their molecularrecognition properties.

International patent application WO 00/75308 discloses muteins of thebilin-binding protein, which specifically bind digoxigenin, whereas theinternational patent applications WO 03/029463 and WO 03/029471 relateto muteins of the human neutrophil gelatinase-associated lipocalin(hNGAL) and apolipoprotein D, respectively. In order to further improveand fine tune ligand affinity, specificity as well as folding stabilityof a lipocalin variant various approaches using different members of thelipocalin family have been proposed (Skerra, A. (2001) Rev. Mol.Biotechnol. 74, 257-275; Schlehuber, S., and Skerra, A. (2002) Biophys.Chem. 96, 213-228), such as the replacement of additional amino acidresidues. The PCT publication WO 2006/56464 discloses muteins of humanneutrophile gelatinase-associated lipocalin with binding affinity forCTLA-4 in the low nanomolar range.

International patent application WO 2005/19256 discloses muteins of tearlipocalin with at least one binding site for different or the sametarget ligand and provides a method for the generation of such muteinsof human tear lipocalin. According to this PCT application, certainamino acid stretches within the primary sequence of tear lipocalin, inparticular the loop regions that include amino acids 7-14, 24-36, 41-49,53-66, 69-77, 79-84, 87-98, and 103-110 of mature human tear lipocalin,are subjected to mutagenesis in order to generate muteins with bindingaffinities. The resulting muteins have binding affinities for theselected ligand (K_(D)) in the nanomolar range, in most cases >100 nM.International patent application WO 2008/015239 discloses muteins oftear lipocalin binding a given non-natural ligand, including the IL-4receptor alpha. Binding affinities are in the nanomolar range, reachingas low as almost 1×10-10 M in surface plamon resonance experiments.

Human tear lipocalin (TLPC or TIc), also termed lipocalin-1, tearpre-albumin or von Ebner gland protein, was originally described as amajor protein of human tear fluid (approximately one third of the totalprotein content) but has also been identified in several other secretorytissues including prostate, adrenal gland, thymus, mammary gland,testis, nasal mucosa and tracheal mucosa as well as corticotrophs of thepituitary gland. Homologous proteins have been found in rhesus monkey,chimpanzee, rat, mouse, pig, hamster, cow, dog and horse. Tear lipocalinis an unusual lipocalin member in that it exhibits an unusually broadligand specificity, when compared to other lipocalins, and in its highpromiscuity for relative insoluble lipids (see Redl, B. (2000) Biochim.Biophys. Acta 1482, 241-248). This feature of tear lipocalin has beenattributed to the protein's function in inhibiting bacterial and fungalgrowth at the cornea. A remarkable number of lipophilic compounds ofdifferent chemical classes such as fatty acids, fatty alcohols,phospholipids, glycolipids and cholesterol are endogenous ligands ofthis protein. Interestingly, in contrast to other lipocalins thestrength of ligand (target) binding correlates with the length of thehydrocarbon tail both for alkyl amides and fatty acids. Thus, tearlipocalin binds most strongly the least soluble lipids (Glasgow, B. J.et al. (1995) Curr. Eye Res. 14, 363-372; Gasymov, O. K. et al. (1999)Biochim. Biophys. Acta 1433, 307-320). The 1.8-Å crystal structure oftear lipocalin revealed an unusually large cavity inside its [β-barrel(Breustedt, D. A. et al. (2005) J. Biol. Chem. 280, 1, 484-493).

Despite this progress it would be still desirable to have a human tearlipocalin mutein that has improved binding properties for IL-4 receptoralpha, in particular of higher binding affinity, simply for the reasonto further improve the suitability of muteins of human tear lipocalin indiagnostic and therapeutic applications.

SUMMARY OF THE INVENTION

Accordingly, it is an object of the invention to provide a further humantear lipocalin mutein with high binding affinity for IL 4 receptoralpha.

This object is accomplished by a human tear lipocalin mutein with thefeatures set out in the claims, in particular in claim 1.

In a first aspect the present invention provides a mutein of human tearlipocalin. The mutein binds to IL 4 receptor alpha. The mutein includesa mutated amino acid residue at any one or more of the sequencepositions 27, 28, 30, 31, 33, 53, 57, 61, 64, 66, 80, 83, 104-106 and108 of the linear polypeptide sequence of the mature human tearlipocalin. The mutein further includes a mutated amino acid residue atany two or more of the sequence positions 26, 32, 34, 55, 56, 58 and 63of the linear polypeptide sequence of the mature human tear lipocalin.The amino acid sequence of the mutein of human tear lipocalin includesone of the following sets of amino acid combinations: (1) Ser 26, Glu34, Leu 55, Lys 58, (2) Ser 26, Asn 34, Ala 55, Lys 58, (3) Ser 26, Val34, (4) Pro 26, Ser 34 (5) Pro 26, Ala 55, (6) Leu 26, Trp 34, Ala 55,(7) Leu 26, Trp 34, Ile 58, (8) Asn 26, Asp 34, (9) Asn 26, Ala 55, (10)Tyr 26, His 34, Ala 55, (11) Tyr 26, His 34, Ala 58, (12) Lys 26, Arg34, Ala 55, (13) Lys 26, Arg 34, Asn 58, (14) Glu 26, Gly 34, Ala 55 and(15) Glu 26, Gly 34, Leu 58.

The term “position” when used in accordance with the invention means theposition of either an amino acid within an amino acid sequence depictedherein or the position of a nucleotide within a nucleic acid sequencedepicted herein. The term “corresponding” as used herein also includesthat a position is not only determined by the number of the precedingnucleotides/amino acids. Accordingly, the position of a given amino acidin accordance with the invention which may be substituted may vary dueto deletion or addition of amino acids elsewhere in a (mutant orwild-type) lipocalin. Similarly, the position of a given nucleotide inaccordance with the present invention which may be substituted may varydue to deletions or additional nucleotides elsewhere in a mutein or wildtype lipocalin 5′-untranslated region (UTR) including the promoterand/or any other regulatory sequences or gene (including exons andintrons).

Thus, under a “corresponding position” in accordance with the inventionit is preferably to be understood that nucleotides/amino acids maydiffer in the indicated number but may still have similar neighboringnucleotides/amino acids. Said nucleotides/amino acids which may beexchanged, deleted or added are also comprised by the term“corresponding position”.

Specifically, in order to determine whether a nucleotide residue oramino acid residue of the amino acid sequence of a lipocalin differentfrom a TIc lipocalin mutein of the invention corresponds to a certainposition in the nucleotide sequence or the amino acid sequence of a TIclipocalin mutein as described, in particular any of SEQ ID NOs: 2-11 orthat having one or more amino acid substitutions at position 27, 28, 30,31, 33, 53, 57, 61, 64, 66, 80, 83, 104-106 and 108 of the linearpolypeptide sequence of TIc (SEQ ID NO: 20), a skilled artisan can usemeans and methods well-known in the art, e.g., alignments, eithermanually or by using computer programs such as BLAST2.0, which standsfor Basic Local Alignment Search Tool or ClustalW or any other suitableprogram which is suitable to generate sequence alignments. Accordingly,a lipocalin mutein of any of SEQ ID Nos: 2-11 or that having one or moreamino acid substitutions at position 27, 28, 30, 31, 33, 53, 57, 61, 64,66, 80, 83, 104-106 and 108 of the linear polypeptide sequence of TIc(SEQ ID NO: 20) can serve as “subject sequence”, while the amino acidsequence of a lipocalin different from TIc serves as “query sequence”.

Ina second aspect the present invention provides a method of generatinga mutein of human tear lipocalin. The mutein binds to IL-4 receptoralpha. The method includes subjecting a nucleic acid molecule encoding ahuman tear lipocalin to mutagenesis at any one or more of the amino acidsequence positions 27, 28, 30, 31, 33, 53, 57, 61, 64, 66, 80, 83,104-106 and 108 of the linear polypeptide sequence of mature human tearlipocalin. Further, the method includes subjecting the nucleic acidmolecule encoding a human tear lipocalin to mutagenesis at any two ormore of the amino acid sequence positions 26, 32, 34, 55, 56, 58 and 63of the linear polypeptide sequence of the mature human tear lipocalin.At least one of the two or more of the amino acid sequence positions 26,32, 34, 55, 56, 58 and 63 of the linear polypeptide sequence of themature human tear lipocalin. As a result one or more nucleic acidsencoding a mutein of human tear lipocalin are obtained. The amino acidsequence of the encoded mutein includes one of the following sets ofamino acid combinations: (1) Ser 26, Glu 34, Leu 55, Lys 58, (2) Ser 26,Asn 34, Ala 55, Lys 58, (3) Ser 26, Val 34, (4) Pro 26, Ser 34, (5) Pro26, Ala 55, (6) Leu 26, Trp 34, Ala 55, (7) Leu 26, Trp 34, Ile 58, (8)Asn 26, Asp 34, (9) Asn 26, Ala 55, (10) Tyr 26, His 34, Ala 55, (11)Tyr 26, His 34, Ala 58, (12) Lys 26, Arg 34, Ala 55, (13) Lys 26, Arg34, Asn 58, (14) Glu 26, Gly 34, Ala 55, and (15) Glu 26, Gly 34, Leu58. The method also includes expressing the one or more mutein encodingnucleic acid molecules thus obtained in an expression system. The methodthereby includes obtaining one or more muteins. Further the methodincludes enriching the one or more muteins thus obtained that bind to IL4 receptor alpha by means of selection and/or isolation.

In a third aspect the present invention provides a nucleic acidmolecule. The nucleic acid molecule includes a nucleotide sequence thatencodes a mutein according to the first aspect.

In a fourth aspect the present invention provides a host cell. The hostcell contains a nucleic acid molecule according to the third aspect.

In a fifth aspect the present invention provides a pharmaceuticalcomposition. The pharmaceutical composition includes a mutein of humantear lipocalin according to the first aspect. The pharmaceuticalcomposition further includes a pharmaceutically acceptable excipient.

The invention will be better understood with reference to the detaileddescription when considered in conjunction with the non-limitingexamples and the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the polypeptide sequence of Si91.4-B24, a mutein of humantear lipocalin possessing binding affinity for the IL-4 receptor alpha.

FIGS. 2A-2F shows the polypeptide sequences of exemplary muteins withhigh affinity for IL-4 receptor alpha (SEQ ID NOs: 2-11).

FIGS. 3A-3B show the inhibition of TF-1 cell proliferation by increasedamounts of muteins of the invention in the presence of IL-4 (A) andIL-13 (B).

FIG. 4 depicts IC₅₀ values of FIG. 3 and data of Biacore® measurementsof the binding of a human tear lipocalin muteins of the invention toIL-4 receptor alpha, such as human IL-4 receptor alpha.

DETAILED DESCRIPTION

The present invention provides muteins of human tear lipocalin that havea particularly high affinity to IL-4 receptor alpha. IL-4 receptor alphaas a target of a mutein of the present invention is typically amammalian protein, such as a human protein. In vivo IL-4 receptor alphacan bind interleukin 4 and interleukin 13 to regulate IgE antibodyproduction in B cells.

Binding affinities of muteins according to the invention have been foundto be typically of a K_(D) below 0.1 nM and in some embodiments about 1picomolar (pM) (cf. FIG. 4). The lipocalin muteins of the invention areaccordingly able to bind IL-4 receptor alpha with detectable affinity,i.e. with a dissociation constant of at least 200 nM. In someembodiments a lipocalin mutein of the invention binds IL-4 receptoralpha with a dissociation constant for IL-4 receptor alpha of at leastabout 10 nM, about 1 nM, about 0.1 nM, about 10 pM or even less. Thebinding affinity of a mutein to a selected target, in the present caseIL-4 receptor alpha, can be measured and thereby K_(D) values of amutein-ligand complex be determine by a multitude of methods known tothose skilled in the art. Such methods include, but are not limited to,fluorescence titration, competition ELISA, calorimetric methods, such asisothermal titration calorimetry (ITC), and surface plasmon resonance(BIAcore®). Examples for such methods are detailed below (See e.g.Example 2).

Human interleukin-4 receptor alpha chain may have the amino acidsequence of SWISS PROT Data Bank Accession No. P24394 (SEQ ID NO: 18) orof fragments thereof. An illustrative example of a fragment of humaninterleukin-4 receptor alpha chain includes amino acids 26 to 232 ofIL-4 receptor alpha. The amino acid sequence of the human IL-13 receptoralpha 1 is shown in SEQ ID NO: 19.

In general, the term “fragment”, as used herein with respect to proteinligands of the tear lipocalin muteins of the invention, relates toN-terminally and/or C-terminally shortened protein or peptide ligands,which retain the capability of the full length ligand to be recognizedand/or bound by a mutein according to the invention.

A human tear lipocalin mutein binding IL-4 receptor alpha may act as anIL-4 antagonist and/or IL-13 antagonist or as an inverse IL-4 agonistand/or inverse IL-13 agonist. An inverse agonist binds to the samebinding-site as an agonist for a particular receptor and reversesconstitutive activity of the respective receptor. So far IL-4 receptorshave not been reported to possess intrinsic kinase activity, so that amutein of the invention may typically act as an IL-4 antagonist and/orIL-13 antagonist. In one embodiment, the human tear lipocalin muteinsact as antagonists of human IL-4 and/or human IL-13. In some embodimentsthe mutein is cross-reactive with the cynomolgus IL-4 IL-4 receptoralpha and as such acts as an antagonist of cynomolgus ligands such asIL-4 and/or IL-13. In some embodiments the mutein is cross-reactive withthe marmoset IL4 IL-4 receptor alpha and as such acts as an antagonistof marmoset ligands such as IL-4 and/or IL-13.

IL4 receptor alpha can be taken to define a non-natural ligand of humantear lipocalin. The term “non-natural ligand” refers to a compound,which does not bind to native mature human tear lipocalin underphysiological conditions. The term “human tear lipocalin” as used hereinrefers to the mature human tear lipocalin corresponding to the proteinof the SWISS-PROT Data Bank Accession Number P31025. Mature human tearlipocalin does not include the N-terminal signal peptide that isincluded in the sequence of SWISS-PROT Accession Number P31025 (seeFIGS. 2A-2F).

The amino acid sequence of a mutein of the invention has a high sequenceidentity to mature human tear lipocalin when compared to sequenceidentities with other lipocalins (supra). In this general context theamino acid sequence of a mutein of the invention is at leastsubstantially similar to the amino acid sequence of mature human tearlipocalin. A respective sequence of a mutein of the invention, beingsubstantially similar to the sequences of mature human tear lipocalin,has in some embodiments at least 70%, at least 75%, at least 80%, atleast 82%, at least 85%, at least 87%, at least 90% identity, includingat least 95% identity to the sequence of mature human tear lipocalin,with the proviso that the altered position or sequence is retained.

By “identity” is meant a property of sequences that measures theirsimilarity or relationship. Identity is measured by dividing the numberof identical residues by the total number of residues and multiplyingthe product by 100. As two illustrative examples, the mutein of the SEQID NO: 3 has a sequence identity of 83.3% with the amino acid sequenceof mature human tear lipocalin, and the mutein of the SEQ ID NO: 7 hasan amino acid sequence identity of 82.0% with mature human tearlipocalin.

“Gaps” are spaces in an alignment that are the result of additions ordeletions of amino acids. Thus, two copies of exactly the same sequencehave 100% identity, but sequences that are less highly conserved, andhave deletions, additions, or replacements, may have a lower degree ofidentity. Those skilled in the art will recognize that several computerprograms are available for determining sequence identity using standardparameters, for example Blast (Altschul, et al. (1997) Nucleic AcidsRes. 25, 3389-3402), Blast2 (Altschul, et al. (1990) J. Mol. Biol. 215,403-410), and Smith-Waterman (Smith, et al. (1981) J. Mol. Biol. 147,195-197).

The term “mutated” or “mutant” in reference to a nucleic acid or apolypeptide refers to the exchange, deletion, or insertion of one ormore nucleotides or amino acids, respectively, compared to the naturallyoccurring nucleic acid or polypeptide. A mutein of the present inventionincludes at least three substitutions in comparison to the correspondingnative human tear lipocalin.

In some embodiments a mutein according to the invention includes atleast two amino acid substitutions, including 2, 3, 4, 5 or more aminoacid substitutions of a native amino acid by an arginine residue. Thesubstituted amino acid may in some embodiments be located at any ofpositions 27, 30, 57 and 83 with respect to the amino acid sequence ofmature human tear lipocalin.

In some embodiments a mutein according to the invention includes anamino acid substitution of a native cysteine residue at positions 61and/or 153 by a serine residue. In this context it is noted that it hasbeen found that removal of the structural disulfide bond (on the levelof a respective naïve nucleic acid library) of wild type tear lipocalinthat is formed by the cystein residues 61 and 153 (cf. Breustedt, etal., 2005, supra) provides tear lipocalin muteins that are not onlystably folded but in addition are also able to bind a given non-naturalligand with high affinity. Without wishing to be bound by theory, it isalso believed that the elimination of the structural disulde bondprovides the further advantage of allowing for the (spontaneous)generation or deliberate introduction of non-natural artifical disulfidebonds into muteins of the invention (see Examples), thereby increasingthe stability of the muteins, for example. In some embodiments a muteinaccording to the invention includes an amino acid substitution of anative cysteine residue at position 101 by a serine residue. Further, insome embodiments a mutein according to the invention includes an aminoacid substitution of a native arginine residue at positions 111 by aproline residue. In some embodiments a mutein according to the inventionincludes an amino acid substitution of a native lysine residue atpositions 114 by a tryptophan residue.

A mutein of human tear lipocalin according to the invention typicallyhas one of an asparagine, a gutamic acid, a proline, a leucine, alysine, a serine and a tyrosine at the position that corresponds toamino acid position 26 of mature human tear lipocalin. In someembodiments a mutein of the invention has a sequence in which amino acidposition 34 is unchanged relative to mature human tear lipocalin, andwhere the sequence of the mutein includes the amino acid substitutionsArg 26→Ser, Met 55→Leu, Ser 58→Lys. In some embodiments a mutein of theinvention has a sequence that includes the amino acid substitutions Arg26→Pro and Glu 34→Ser. In some embodiments a mutein of the invention hasa sequence that includes the amino acid substitutions Arg 26→Pro and Met55→Ala. In some embodiments a mutein of the invention has a sequencethat includes the amino acid substitutions Arg 26→Ser and Glu 34→Val. Insome embodiments a mutein of the invention has a sequence that includesthe amino acid substitutions Arg 26→Leu, Glu 34→Trp and Met 55→Ala. Insome embodiments a mutein of the invention has a sequence that includesthe amino acid substitutions Arg 26→Leu, Glu 34→Trp and Ser 58→Ile. Insome embodiments a mutein of the invention has a sequence that includesthe amino acid substitutions Arg 26→Ser, Glu 34→Asn, Met 55→Ala, and Ser58→Lys. In some embodiments a mutein of the invention has a sequencethat includes the amino acid substitutions Arg 26→Asn and Glu 34→Asp. Insome embodiments a mutein of the invention has a sequence that includesthe amino acid substitutions Arg 26→Asn and Met 55→Ala. In someembodiments a mutein of the invention has a sequence that includes theamino acid substitutions Arg 26→Tyr, Glu 34→His and Met 55→Ala. In someembodiments a mutein of the invention has a sequence that includes theamino acid substitutions Arg 26→Tyr, Glu 34→His and Ser 58→Ala. In someembodiments a mutein of the invention has a sequence that includes theamino acid substitutions Arg 26→Lys, Glu 34→Arg and Met 55→Ala. In someembodiments a mutein of the invention has a sequence that includes theamino acid substitutions Arg 26→Lys, Glu 34→Arg and Ser 58→Asn. In someembodiments a mutein of the invention has a sequence that includes theamino acid substitutions Arg 26→Glu, Glu 34→Arg and Met 55→Ala. In someembodiments a mutein of the invention has a sequence that includes theamino acid substitutions Arg 26→Glu, Glu 34→Arg and Ser 58→Leu.

In some embodiments a human tear lipocalin mutein of the invention thatbinds IL-4 receptor alpha has, when compared to the amino acid sequenceof mature human tear lipocalin, a mutated amino acid residue at sequenceposition 58 or at sequence position 63. In some embodiments the sequenceof the mutein of the invention is selected in such a way that, whencompared to the amino acid sequence of mature human tear lipocalin, notat both amino acid positions 26 and 34 a serine is present.

The lipocalin mutein may further include with respect to the amino acidsequence of mature human tear lipocalin one or more, including at leasttwo, at least three or at least four amino acid substitutions of nativeamino acid residues by cysteine residues at any of positions 26-28,30-34, 53, 55-58, 61, 63, 64, 66, 80, 83, 104-106, and 108 of nativemature human tear lipocalin. In some embodiments a mutein according tothe invention includes an amino acid substitution of a native amino acidby a cysteine residue at positions 28 or 105 with respect to the aminoacid sequence of mature human tear lipocalin. In some embodiments amutein according to the invention includes an amino acid substitution ofa native amino acid by a cysteine residue at positions 28 or 105 withrespect to the amino acid sequence of mature human tear lipocalin.

In some embodiments a mutein according to the invention includes amutated amino acid residue at any three or more, including 3, 4, 5, 6 or7, of the sequence positions 26, 32, 34, 55, 56, 58 and 63 of the linearpolypeptide sequence of the mature human tear lipocalin.

In some embodiments the lipocalin mutein of the invention has a mutatedamino acid residue at position 26 that is one of asparagine, glutamine,proline, leucine, lysine, serine and tyrosine. In some embodiments thelipocalin mutein of the invention has a mutated amino acid residue atposition 32 that is one of histidine, lysine, tyrosine and valine. Insome embodiments the lipocalin mutein of the invention has a mutatedamino acid residue at position 34 that is one of arginine, asparticacid, asparagine, histidine, serine, tryptophan and valine. In someembodiments the lipocalin mutein of the invention has a mutated aminoacid residue at position 55 that is one of alanine and leucine. In someembodiments the lipocalin mutein of the invention has a mutated aminoacid residue at position 56 that is one of alanine, glutamine,histidine, methionine, leucine and lysine. In some embodiments thelipocalin mutein of the invention has a mutated amino acid residue atposition 58 that is one of alanine, arginine, asparagine, histidine,isoleucine and lysine. In some embodiments the lipocalin mutein of theinvention has a mutated amino acid residue at position 63 that is one ofglutamine, lysine, proline and serine.

In some embodiments a mutein according to the invention includes atleast one of the substitutions Met 31→Ala, Leu 33→Tyr, Ser 61→Trp, Asp80→Ser, Glu 104→Leu, His 106→Pro and Lys 108→Gln. In some embodiments amutein according to the invention includes two or more, such as 3, 4, 5,6 or all of the substitutions Met 31→Ala, Leu 33→Tyr, Ser 61→Trp, Asp80→Ser, Glu 104→Leu, His 106→Pro and Lys 108→Gln. In some embodiments amutein according to the invention includes a substitution Val 53→Phe orVal 53→Leu. The mutated amino acid residue may also include asubstitution Val 64→Tyr or Val 64→Met. It may also include asubstitution Ala 66→Leu or Ala 66→Asp.

In some embodiments a mutein of human tear lipocalin according to theinvention includes a substituted amino acid of at least one or of bothof the cysteine residues occurring at each of the sequences positions 61and 153 by another amino acid and the mutation of at least three aminoacid residue at any one of the sequence positions 26-28, 30-34, 53,55-58, 63, 64, 66, 80, 83, 104-106, and 108 of the linear polypeptidesequence of mature human tear lipocalin. The positions 26-28 and 30-34are included in the AB loop, the positions 53 and 55 are located at thevery end of a beta-sheet and following positions 56-58 are included inthe CD loop. Surprisingly, the positions 63, 64 and 66, are includedwithin a beta-sheet (βD), and the position 80 is located in a α-helicalregion. Position 83 is a single loop-defining amino acid between thisα-helical region and a beta-sheet (βF). The positions 104-106 and 108are included in the GH loop in the binding site at the open end of theβ-barrel structure of tear lipocalin. The definition of these regions isused herein in accordance with Flower (Flower, 1996, supra, Flower, etal., 2000, supra) and Breustedt et al. (2005, supra). Such a mutein mayinclude at least 2, including 3, 4, 5, 6, 8, 10, 12, 14, 15, 16, 17 or18 mutated amino acid residues at the sequence positions 26-34, 55-58,63, 64, 80, 83, 104-106, and 108 of the linear polypeptide sequence ofmature human tear lipocalin. In some embodiments the mutein includes theamino acid substitutions Cys 61→Ala, Phe, Lys, Arg, Thr, Asn, Tyr, Met,Ser, Pro or Trp and Cys 153→Ser or Ala. Such a substitution has provenuseful to prevent the formation of the naturally occurring disulphidebridge linking Cys 61 and Cys 153, and thus to facilitate handling ofthe mutein. However, tear lipocalin muteins that binds IL-4 receptoralpha and that have the disulphide bridge formed between Cys 61 and Cys153 are also part of the present invention

In some embodiments the mutein includes at least one amino acidsubstitution, which may be an additional amino acid substitution,selected from Arg 111→Pro and Lys 114→Trp. A mutein of the invention mayfurther include the cysteine at position 101 of the sequence of nativemature human tear lipocalin substituted by another amino acid. Thissubstitution may, for example, be the mutation Cys 101→Ser or Cys101→Thr.

As defined above, a mutein of the invention includes at least one aminoacid substitution, which is located at a sequence position of thepositions 27, 28, 30, 31, 33, 53, 57, 61, 64, 66, 80, 83, 104-106 and108 of the linear polypeptide sequence of the mature human tearlipocalin. In some embodiments a mutein of the invention includes two ormore, such as 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 1, 15 or 16 aminoacid substitutions of these sequence positions of the mature human tearlipocalin. In one embodiment the mutein has a mutated amino acid residueat each of the sequence positions 27, 28, 30, 31, 33, 53, 57, 61, 64,66, 80, 83, 104-106 and 108 of the linear polypeptide sequence of themature human tear lipocalin.

In some embodiments the mutated amino acid residue at any one or more ofthe sequence positions 27, 28, 30, 31, 33, 53, 57, 61, 64, 66, 80, 83,104-106 and 108 of the linear polypeptide sequence of the mature humantear lipocalin with respect to the amino acid sequence of mature humantear lipocalin includes one or more of the substitutions Met 31→Ala, Leu33→Tyr, Ser 61→Trp, Asp 80→Ser, Glu 104→Leu, His 106→Pro and Lys108→Gln. In some embodiments a mutein of the invention includes two ormore, such as 3, 4, 5, 6 or 7 amino acid substitutions of these sequencepositions of the mature human tear lipocalin.

In the residual region, i.e. the region differing from sequencepositions 26-28, 30-34, 53, 55-58, 63, 64, 66, 80, 83, 104-106, and 108,a lipocalin mutein of the invention may include the wild type (natural)amino acid sequence outside the mutated amino acid sequence positions.In some embodiments a lipocalin mutein according to the invention mayalso carry one or more amino acid mutations at a sequenceposition/positions as long as such a mutation does, at least essentiallynot hamper or not interfere with the binding activity and the folding ofthe mutein. Such mutations can be accomplished very easily on DNA levelusing established standard methods. Illustrative examples of alterationsof the amino acid sequence are insertions or deletions as well as aminoacid substitutions. Such substitutions may be conservative, i.e. anamino acid residue is replaced with an amino acid residue of chemicallysimilar properties, in particular with regard to polarity as well assize. Examples of conservative substitutions are the replacements amongthe members of the following groups: 1) alanine, serine, and threonine;2) aspartic acid and glutamic acid; 3) asparagine and glutamine; 4)arginine and lysine; 5) isoleucine, leucine, methionine, and valine; and6) phenylalanine, tyrosine, and tryptophan. On the other hand, it isalso possible to introduce non-conservative alterations in the aminoacid sequence. In addition, instead of replacing single amino acidresidues, it is also possible to either insert or delete one or morecontinuous amino acids of the primary structure of tear lipocalin aslong as these deletions or insertion result in a stablefolded/functional mutein (see for example, the experimental section inwhich muteins with truncated N- and C-terminus are generated).

Such modifications of the amino acid sequence include directedmutagenesis of single amino acid positions in order to simplifysub-cloning of the mutated lipocalin gene or its parts by incorporatingcleavage sites for certain restriction enzymes. In addition, thesemutations can also be incorporated to further improve the affinity of alipocalin mutein for a given target. Furthermore, mutations can beintroduced in order to modulate certain characteristics of the muteinsuch as to improve folding stability, serum stability, proteinresistance or water solubility or to reduce aggregation tendency, ifnecessary. For example, naturally occurring cysteine residues may bemutated to other amino acids to prevent disulphide bridge formation. Itis also possible to deliberately mutate other amino acid sequenceposition to cysteine in order to introduce new reactive groups, forexample for the conjugation to other compounds, such as polyethyleneglycol (PEG), hydroxyethyl starch (HES), biotin, peptides or proteins,or for the formation of non-naturally occurring disulphide linkages.Exemplary possibilities of such a mutation to introduce a cysteineresidue into the amino acid sequence of a human tear lipocalin muteininclude the substitutions Thr 40→Cys, Glu 73→Cys, Arg 90→Cys, Asp95→Cys, and Glu 131→Cys. The generated thiol moiety at the side of anyof the amino acid positions 40, 73, 90, 95 and/or 131 may be used toPEGylate or HESylate the mutein, for example, in order to increase theserum half-life of a respective tear lipocalin mutein.

The present invention also encompasses muteins as defined above, inwhich the first four N-terminal amino acid residues of the sequence ofmature human tear lipocalin (His-His-Leu-Leu; positions 1-4) and/or thelast two C-terminal amino acid residues (Ser-Asp; positions 157-158) ofthe sequence of mature human tear lipocalin have been deleted (cf. alsothe Examples and the attached Sequence Listings). Another possiblemutation of the wild type sequence is to change the amino acid sequenceat sequence positions 5 to 7 (Ala Ser Asp) to Gly Gly Asp as describedin PCT application WO 2005/019256.

In some embodiments a tear lipocalin mutein according to the inventionhas one or more, including 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 of thefollowing amino acid substitutions in comparison to mature human tearlipocalin: Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met 31→Ala; Leu 33→Tyr;Ile 57→Arg; Ser 61→Trp; Asp 80→Ser; Lys 83→Arg; Glu 104→Leu; Leu105→Cys; His 106→Pro; Lys 108→Gln. In some embodiments the muteinincludes all of these amino acid substitutions. In some embodiments themutein further includes the set of amino acid substitutions Val 53→Phe,Val 64→Tyr, Ala 66→Leu. In other embodiments the mutein further includesthe set of amino acid substitutions Val 53→Leu, Val 64→Met, Ala 66→Asp.

In some embodiments a tear lipocalin mutein according to the inventionincludes the combination of amino acid substitutions Arg 26→Ser; Asn32→Tyr; Met 55→Leu; Leu 56→Gln; Ser 58→Lys in comparison to mature humantear lipocalin. In some embodiments a tear lipocalin mutein according tothe invention includes the combination of amino acid substitutions Arg26→Pro; Asn 32→Tyr; Glu 34→Ser; Met 55→Ala; Leu 56→Gln; Glu 63→Lys incomparison to mature human tear lipocalin. In some embodiments a tearlipocalin mutein according to the invention includes the combination ofamino acid substitutions Arg 26→Leu; Asn 32→Phe; Glu 34→Trp; Met 55→Ala;Ser 58→Ile; Glu 63→Ser in comparison to mature human tear lipocalin. Insome embodiments a tear lipocalin mutein according to the inventionincludes the combination of amino acid substitutions Arg 26→Ser; Asn32→Tyr; Glu 34→Val; Met 55→Ala; Leu 56→Ala; Ser 58→Ile; Glu 63→Ser incomparison to mature human tear lipocalin. In some embodiments a tearlipocalin mutein according to the invention includes the combination ofamino acid substitutions Arg 26→Ser; Asn 32→Val; Glu 34→Asn; Met 55→Ala;Leu 56→Gln; Ser 58→Lys; Glu 63→Lys in comparison to mature human tearlipocalin. In some embodiments a tear lipocalin mutein according to theinvention includes the combination of amino acid substitutions Arg26→Tyr; Asn 32→Tyr; Glu 34→His; Met 55→Ala; Leu 56→His; Ser 58→Ala; Glu63→Lys in comparison to mature human tear lipocalin. In some embodimentsa tear lipocalin mutein according to the invention includes thecombination of amino acid substitutions Arg 26→Lys; Asn 32→Tyr; Glu34→Arg; Met 55→Ala; Leu 56→Lys; Ser 58→Asn; Glu 63→Pro in comparison tomature human tear lipocalin. In some embodiments a tear lipocalin muteinaccording to the invention includes the combination of amino acidsubstitutions Arg 26→Glu; Asn 32→His; Glu 34→Gly; Met 55→Ala; Leu56→Met; Ser 58→Leu; Glu 63→Lys in comparison to mature human tearlipocalin.

In some embodiments a mutein of the invention includes with respect tothe amino acid sequence of mature human tear lipocalin at least 6, 8,10, 12, 14 or 16 amino acid substitutions selected from the groupconsisting of Arg 26→Ser, Pro; Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met31→Ala; Asn 32→Tyr, His; Leu 33→Tyr; Glu 34→Gly, Ser, Ala, Asp, Lys,Asn, Thr, Arg; Leu 56→Gln; Ile 57→Arg; Ser 58→Ile, Ala, Arg, Val, Thr,Asn, Lys, Tyr, Leu, Met; Asp 80→Ser; Lys 83→Arg; Glu 104→Leu; Leu105→Cys; His 106→Pro; and Lys 108→Gln.

Additionally, such a mutein may further include at least one amino acidsubstitution selected from the group consisting of Met 39→Val; Thr42→Met, Ala; Thr 43→Ile, Pro, Ala; Glu 45→Lys, Gly; Asn 48→Asp, His,Ser, Thr; Val 53→Leu, Phe, Ile, Ala, Gly, Ser; Thr 54→Ala, Leu; Met55→Leu, Ala, Ile, Val, Phe, Gly, Thr, Tyr; Glu 63→Lys, Gln, Ala, Gly,Arg; Val 64→Gly, Tyr, Met, Ser, Ala, Lys, Arg, Leu, Asn, His, Thr, Ile;Ala 66→Ile, Leu, Val, Thr, Met; Glu 69→Lys, Gly; Lys 70→Arg, Gln, Glu;Thr 78→Ala; Ile 89→Val; Asp 95→Asn, Ala, Gly; and Tyr 100→His.

In one embodiment the human tear lipocalin mutein binding IL-4 receptoralpha includes the amino acid substitutions: Arg 26→Ser, Glu 27→Arg, Phe28→Cys, Glu 30→Arg; Met 31→Ala, Leu 33→Tyr, Leu 56→Gln, Ile 57→Arg, Asp80→Ser, Lys 83→Arg, Glu 104→Leu, Leu 105→Cys, His 106→Pro, and Lys108→Gln.

In some embodiments the human tear lipocalin mutein binding IL-4receptor alpha includes one of the following sets of amino acidsubstitutions:

(1) Arg 26→Ser; Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met 31→Ala; Asn32→Tyr; Leu 33→Tyr; Glu 34→Gly; Leu 56→Gln; Ile 57→Arg; Ser 58→Ile; Asp80→Ser; Lys 83→Arg; Glu 104→Leu; Leu 105→Cys; His 106→Pro; Lys 108→Gln;(2) Arg 26→Ser; Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met 31→Ala; Asn32→Tyr; Leu 33→Tyr; Glu 34→Lys; Leu 56→Gln; Ile 57→Arg; Ser 58→Asn; Asp80→Ser; Lys 83→Arg; Giu 104→Leu; Leu 105→Cys; His 106→Pro; Lys 108→Gln;(3) Arg 26→Ser; Glu 27→Arg; Phe 28→Cys, Glu 30→Arg; Met 31 Ala; Asn32→Tyr; Leu 33→Tyr; Leu 56→Gln; Ile 57→Arg; Ser 58→Arg; Asp 80→Ser; Lys83→Arg; Glu 104→Leu; Leu 105→Cys; His 106→Pro; Lys 108→Gln;(4) Arg 26→Ser; Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met 31→Ala; Asn32→Tyr; Leu 33→Tyr; Glu 34 Ser; Leu 56→Gln; lie 57→Arg; Asp 80→Ser; Lys83 Arg; Glu 104→Leu; Leu 105→Cys; His 106→Pro; Lys 108→Gln;(5) Arg 26→Ser; Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met 31→Ala; Asn32→His; Leu 33→Tyr; Glu 34→Ser; Leu 56→Gln; le 57→Arg; Ser 58→Ala; Asp80→Ser; Lys 83→Arg; Glu 104→Leu; Leu 105→Cys; His 106→Pro; Lys 108→Gln;(6) Arg 26→Ser; Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met 31→Ala; Asn 32Tyr; Leu 33→Tyr; Glu 34→Asp; Leu 56→Gln; Ile 57→Arg; Ser 58→Lys; Asp80→Ser; Lys 83→Arg; Glu 104→Leu; Leu 105→Cys; His 106→Pro; Lys 108→Gln;and(7) Arg 26→Ser; Glu 27→Arg; Phe 28→Cys; Glu 30→Arg; Met 31→Ala; Asn32→Tyr; Leu 33→Tyr; Glu 34 Gly; Leu 56→Gln; Ile 57→Arg; Asp 80→Ser; Lys83→Arg; Glu 104→Leu; Leu 105→Cys; His 106→Pro; Lys 108→Gln.

The human tear lipocalin mutein of the invention may include, consistessentially of or consist of any one of the amino acid sequences setforth in SEQ ID NOs: 3-11 or a fragment or variant thereof. The term“fragment” as used herein in connection with the muteins of theinvention relates to proteins or peptides derived from full-lengthmature human tear lipocalin that are N-terminally and/or C-terminallyshortened, i.e. lacking at least one of the N-terminal and/or C-terminalamino acids. Such fragments may include at least 10, more such as 20 or30 or more consecutive amino acids of the primary sequence of maturehuman tear lipocalin and are usually detectable in an immunoassay ofmature human tear lipocalin.

The term “variant” as used in the present invention relates toderivatives of a protein or peptide that include modifications of theamino acid sequence, for example by substitution, deletion, insertion orchemical modification. Such modifications do in some embodiments notreduce the functionality of the protein or peptide. Such variantsinclude proteins, wherein one or more amino acids have been replaced bytheir respective D-stereoisomers or by amino acids other than thenaturally occurring 20 amino acids, such as, for example, ornithine,hydroxyproline, citrulline, homoserine, hydroxylysine, norvaline.However, such substitutions may also be conservative, i.e. an amino acidresidue is replaced with a chemically similar amino acid residue.Examples of conservative substitutions are the replacements among themembers of the following groups: 1) alanine, serine, and threonine; 2)aspartic acid and glutamic acid; 3) asparagine and glutamine; 4)arginine and lysine; 5) isoleucine, leucine, methionine, and valine; and6) phenylalanine, tyrosine, and tryptophan.

Such a mutein may include with respect to the amino acid sequence ofmature human tear lipocalin at least 6, 8, 10, 12, 14 or 16 amino acidsubstitutions selected from the group consisting of Arg 26→Ser; Glu27→Ile; Glu 30→Ser; Met 31→Gly; Asn 32→Arg; Leu 33→Ile; Glu34→Tyr;Leu56→Lys, Glu, Ala, Met; Ile57→Phe; Ser58→Arg; Asp80→Ser, Pro; Lys 83Glu, Gly; Glu 104→Leu; Leu 105→Ala; His 106→Val; and Lys 108→Thr and mayfurther include at least one amino acid substitution selected from thegroup consisting of Leu 41→Phe; Glu 63→Lys; Val 64→Met; Asp 72→Gly; Lys76→Arg, Glu; Ile 88→Val, Thr; Ile 89→Thr; Arg 90→Lys; Asp 95→Gly; Phe99→Leu; and Gly 107→Arg, Lys, Glu.

In one specific embodiment, such a mutein includes the amino acidsubstitutions: Arg 26→Ser, Glu27→Ile, Glu30→Ser, Met31→Gly, Asn32→Arg,Leu33→Ile, Glu34→Tyr, Ile 57→Phe, Ser 58→Arg, Lys 83→Glu, Glu 104→Leu,Leu 105→Ala, His 106→Val, and Lys 108→Thr.

A tear lipocalin mutein of the invention may exist as a monomericprotein. In some embodiments a lipocalin mutein according to theinvention may be able to spontaneously dimerise or oligomerise. The useof lipocalin muteins that form stable monomers may be advantageous insome applications, e.g. because of faster diffusion and better tissuepenetration. In other embodiments the use of a lipocalin mutein thatspontaneously forms stable homodimers or multimers may be advantageous,since such multimers can provide (further) increased affinity and/oravidity to a given target. Furthermore, oligomeric forms of thelipocalin mutein may have slower dissociation rates or prolonged serumhalf-life. If dimerisation or multimerisation of muteins that formstable monomers is desired, this can for example be achieved by fusingrespective oligomerization domains such as jun-fos domains orleucin-zippers to muteins of the invention or by the use of “Duocalins”(see also below).

A lipocalin mutein according to the present invention can be obtained bymeans of mutagenesis of a naturally occurring form of human tearlipocalin. The term “mutagenesis” as used herein means that theexperimental conditions are chosen such that the amino acid naturallyoccurring at a given sequence position of human tear lipocalin(Swiss-Prot data bank entry P31025) can be substituted by at least oneamino acid that is not present at this specific position in therespective natural polypeptide sequence. The term “mutagenesis” alsoincludes the (additional) modification of the length of sequencesegments by deletion or insertion of one or more amino acids. Thus, itis within the scope of the invention that, for example, one amino acidat a chosen sequence position is replaced by a stretch of three randommutations, leading to an insertion of two amino acid residues comparedto the length of the respective segment of the wild type protein. Suchan insertion of deletion may be introduced independently from each otherin any of the peptide segments that can be subjected to mutagenesis inthe invention. In one exemplary embodiment of the invention, aninsertion of several mutations may be introduced into the loop AB of thechosen lipocalin scaffold (cf. International Patent Application WO2005/019256 which is incorporated by reference its entirety herein). Theterm “random mutagenesis” means that no predetermined single amino acid(mutation) is present at a certain sequence position but that at leasttwo amino acids can be incorporated with a certain probability at apredefined sequence position during mutagenesis.

The coding sequence of human tear lipocalin (Redl, B. et al. (1992) J.Biol. Chem. 267, 20282-20287) is used as a starting point for themutagenesis of the peptide segments selected in the present invention.For the mutagenesis of the recited amino acid positions, the personskilled in the art has at his disposal the various established standardmethods for site-directed mutagenesis. A commonly used technique is theintroduction of mutations by means of PCR (polymerase chain reaction)using mixtures of synthetic oligonucleotides, which bear a degeneratebase composition at the desired sequence positions. For example, use ofthe codon NNK or NNS (wherein N=adenine, guanine or cytosine or thymine;K=guanine or thymine; S=adenine or cytosine) allows incorporation of all20 amino acids plus the amber stop codon during mutagenesis, whereas thecodon VVS limits the number of possibly incorporated amino acids to 12,since it excludes the amino acids Cys, le, Leu, Met, Phe, Trp, Tyr, Valfrom being incorporated into the selected position of the polypeptidesequence; use of the codon NMS (wherein M=adenine or cytosine), forexample, restricts the number of possible amino acids to 11 at aselected sequence position since it excludes the amino acids Arg, Cys,Gly, Ile, Leu, Met, Phe, Trp, Val from being incorporated at a selectedsequence position. In this respect it is noted that codons for otheramino acids (than the regular 20 naturally occurring amino acids) suchas selenocystein or pyrrolysine can also be incorporated into a nucleicacid of a mutein. It is also possible, as described by Wang, L., et al.(2001) Science 292, 498-500, or Wang, L., and Schultz, P. G. (2002)Chem. Comm. 1, 1-11, to use “artificial” codons such as UAG which areusually recognized as stop codons in order to insert other unusual aminoacids, for example o-methyl-L-tyrosine or p-aminophenylalanine.

The use of nucleotide building blocks with reduced base pairspecificity, as for example inosine, 8-oxo-2′deoxyguanosine or6(2-deoxy-E-D-ribofuranosyl)-3,4-dihydro-8H-pyrimindo-1,2-oxazine-7-one(Zaccolo et al. (1996) J. Mol. Biol. 255, 589-603), is another optionfor the introduction of mutations into a chosen sequence segment.

A further possibility is the so-called triplet-mutagenesis. This methoduses mixtures of different nucleotide triplets, each of which codes forone amino acid, for incorporation into the coding sequence (Virnekis B,et al., 1994 Nucleic Acids Res 22, 5600-5607).

One possible strategy for introducing mutations in the selected regionsof the respective polypeptides is based on the use of fouroligonucleotides, each of which is partially derived from one of thecorresponding sequence segments to be mutated. When synthesizing theseoligonucleotides, a person skilled in the art can employ mixtures ofnucleic acid building blocks for the synthesis of those nucleotidetriplets which correspond to the amino acid positions to be mutated sothat codons encoding all natural amino acids randomly arise, which atlast results in the generation of a lipocalin peptide library. Forexample, the first oligonucleotide corresponds in its sequence—apartfrom the mutated positions—to the coding strand for the peptide segmentto be mutated at the most N-terminal position of the lipocalinpolypeptide. Accordingly, the second oligonucleotide corresponds to thenon-coding strand for the second sequence segment following in thepolypeptide sequence. The third oligonucleotide corresponds in turn tothe coding strand for the corresponding third sequence segment. Finally,the fourth oligonucleotide corresponds to the non-coding strand for thefourth sequence segment. A polymerase chain reaction can be performedwith the respective first and second oligonucleotide and separately, ifnecessary, with the respective third and fourth oligonucleotide.

The amplification products of both of these reactions can be combined byvarious known methods into a single nucleic acid that includes thesequence from the first to the fourth sequence segments, in whichmutations have been introduced at the selected positions. To this end,both of the products can for example be subjected to a new polymerasechain reaction using flanking oligonucleotides as well as one or moremediator nucleic acid molecules, which contribute the sequence betweenthe second and the third sequence segment. In the choice of the numberand arrangement within the sequence of the oligonucleotides used for themutagenesis, the person skilled in the art has numerous alternatives athis disposal.

The nucleic acid molecules defined above can be connected by ligationwith the missing 5′- and 3′-sequences of a nucleic acid encoding alipocalin polypeptide and/or the vector, and can be cloned in a knownhost organism. A multitude of established procedures are available forligation and cloning. For example, recognition sequences for restrictionendonucleases also present in the sequence of the cloning vector can beengineered into the sequence of the synthetic oligonucleotides. Thus,after amplification of the respective PCR product and enzymatic cleavagethe resulting fragment can be easily cloned using the correspondingrecognition sequences.

Longer sequence segments within the gene coding for the protein selectedfor mutagenesis can also be subjected to random mutagenesis via knownmethods, for example by use of the polymerase chain reaction underconditions of increased error rate, by chemical mutagenesis or by usingbacterial mutator strains. Such methods can also be used for furtheroptimization of the target affinity or specificity of a lipocalinmutein. Mutations possibly occurring outside the segments ofexperimental mutagenesis are often tolerated or can even prove to beadvantageous, for example if they contribute to an improved foldingefficiency or folding stability of the lipocalin mutein.

In a method according to the invention a nucleic acid molecule encodinga human tear lipocalin is firstly subjected to mutagenesis at one ormore of the amino acid sequence positions 27, 28, 30, 31, 33, 53, 57,61, 64, 66, 80, 83, 104-106 and 108 of the linear polypeptide sequenceof mature human tear lipocalin. Secondly the nucleic acid moleculeencoding a human tear lipocalin is also subjected to mutagenesis at twoor more of the amino acid sequence positions 26, 32, 34, 55, 56, 58 and63 of the linear polypeptide sequence of the mature human tearlipocalin. Of these latter amino acid sequence positions at least oneposition to be mutated is selected from amino acid sequence position 58and amino acid sequence position 63.

In one embodiment of the invention, the method for the generation of amutein of human tear lipocalin includes mutating at least 2, 3, 4, 5, 6,8, 10, 12, 14, 15, 16, or 17 of the codons of any of the amino acidsequence positions 26-28, 30-34, 53, 55-58, 63, 64, 66, 80, 83, 104-106,and 108 of the linear polypeptide sequence of mature human tearlipocalin. In one embodiment all 22 of the codons of amino acid sequencepositions 26, 27, 28, 30, 31, 32, 33, 34, 53, 55, 56, 57, 58, 63, 64,66, 80, 83, 104, 105, 106, and 108 of the linear polypeptide sequence ofmature human tear lipocalin are mutated.

In one embodiment of the afore-mentioned method, additionally at least2, 3, 4, 5, 6, 8, 10, 12, 14, or 15 of the codons of any of the aminoacid sequence positions 26-28, 30-34, 53, 55-58, 63, 64, 66, 80, 83,104-106, and 108 of the linear polypeptide sequence of mature human tearlipocalin are mutated.

In a further embodiment of the invention, the methods according to theinvention include the mutation of both of the codons encoding cysteineat positions 61 and 153 in the linear polypeptide sequence of maturehuman tear lipocalin. In one embodiment position 61 is mutated to encodean alanine, phenylalanine, lysine, arginine, threonin, asparagine,tyrosine, methionine, serine, proline or a tryptophane residue, to nameonly a few possibilities. In embodiments where position 153 is mutated,an amino acid such as a serine or alanine can be introduced at position153.

In another embodiment of the invention as described herein, the codonsencoding amino acid sequence positions 111 and/or 114 of the linearpolypeptide sequence of mature human tear lipocalin are mutated toencode for example an arginine at position 111 and a tryptophane atposition 114.

Another embodiment of the methods of the invention, involves mutagenesisof the codon encoding the cysteine at position 101 of the linearpolypeptide sequence of mature human tear lipocalin so that this codonencodes any other amino acid. In one embodiment the mutated codonencoding position 101 encodes a serine. Accordingly, in some embodimentseither two or all three of the cystein codons at position 61, 101 and153 are replaced by a codon of another amino acid.

According to the method of the invention a mutein is obtained startingfrom a nucleic acid encoding human tear lipocalin. Such a nucleic acidis subjected to mutagenesis and introduced into a suitable bacterial oreukaryotic host organism by means of recombinant DNA technology.Obtaining a nucleic acid library of tear lipocalin can be carried outusing any suitable technique that is known in the art for generatinglipocalin muteins with antibody-like properties, i.e. muteins that haveaffinity towards a given target. Examples of such combinatorial methodsare described in detail in the international patent applications WO99/16873, WO 00/75308, WO 03/029471, WO 03/029462, WO 03/029463, WO2005/019254, WO 2005/019255, WO 2005/019256, or WO 2006/56464 forinstance. The content of each of these patent applications isincorporated by reference herein in its entirety. After expression ofthe nucleic acid sequences that were subjected to mutagenesis in anappropriate host, the clones carrying the genetic information for theplurality of respective lipocalin muteins, which bind a given target canbe selected from the library obtained. Well known techniques can beemployed for the selection of these clones, such as phage display(reviewed in Kay, B. K. et al. (1996) supra; Lowman, H. B. (1997) supraor Rodi, D. J., and Makowski, L. (1999) supra), colony screening(reviewed in Pini, A. et al. (2002) Comb. Chem. High Throughput Screen.5, 503-510), ribosome display (reviewed in Amstutz, P. et al. (2001)Curr. Opin. Biotechnol. 12, 400-405) or mRNA display as reported inWilson, D. S. et al. (2001) Proc. Natl. Acad. Sci. USA 98, 3750-3755 orthe methods specifically described in WO 99/16873, WO 00/75308, WO03/029471, WO 03/029462, WO 03/029463, WO 2005/019254, WO 2005/019255,WO 2005/019256, or WO 2006/56464.

The nucleic acid molecule encoding the mutein is expressed using anysuitable expression system. The obtained mutein or muteins is/areenriched by means of selection and/or isolation. The selection may forexample be carried out under competitive conditions. Competitiveconditions as used herein means that selection of muteins encompasses atleast one step in which the muteins and the given non-natural ligand ofhuman tear lipocalin, i.e. the IL 4 receptor alpha, are brought incontact in the presence of an additional ligand, which competes withbinding of the muteins to IL 4 receptor alpha. This additional ligandmay be a physiological ligand of the target, e.g. IL 4, an excess of thetarget itself or any other non-physiological ligand of the target thatbinds at least an overlapping epitope to the epitope recognized by themuteins of the invention and thus interferes with target binding of themuteins. Alternatively, the additional ligand competes with binding ofthe muteins by complexing an epitope distinct from the binding site ofthe muteins to the target by allosteric effects.

An embodiment of the phage display technique (reviewed in Kay, B. K. etal. (1996), supra; Lowman, H. B. (1997) supra or Rodi, D. J., &Makowski, L. (1999), supra) using temperent M13 phage is given as anexample of a selection method that can be employed in the presentinvention. Another embodiment of the phage display technology that canbe used for selection of muteins of the invention is the hyperphagephage technology as described by Broders et al. (Broders et al. (2003)“Hyperphage. Improving antibody presentation in phage display.” MethodsMol. Biol. 205:295-302). Other temperent phage such as f1 or lytic phagesuch as T7 may be employed as well. For the exemplary selection method,M13 phagemids are produced which allow the expression of the mutatedlipocalin nucleic acid sequence as a fusion protein with a signalsequence at the N-terminus, such as the OmpA-signal sequence, and withthe capsid protein pill of the phage M13 or fragments thereof capable ofbeing incorporated into the phage capsid at the C-terminus. TheC-terminal fragment ΔpIII of the phage capsid protein that includesamino acids 217 to 406 of the wild type sequence is may be used toproduce the fusion proteins. In one embodiment a C-terminal fragment ofpIII is used, in which the cysteine residue at position 201 is missingor is replaced by another amino acid.

Accordingly, a further embodiment of the methods of the inventioninvolves operably fusing a nucleic acid coding for the one or moremuteins of human tear lipocalin and resulting from mutagenesis at the 3′end with a gene coding for the coat protein pIII of a filamentousbacteriophage of the M13-family or for a fragment of this coat protein,in order to select at least one mutein for the binding of a givenligand.

The fusion protein may include additional components such as an affinitytag, which allows the immobilization, detection and/or purification ofthe fusion protein or its parts. Furthermore, a stop codon can belocated between the sequence regions encoding the lipocalin or itsmuteins and the phage capsid gene or fragments thereof, wherein the stopcodon, such as an amber stop codon, is at least partially translatedinto an amino acid during translation in a suitable suppressor strain.

For example, the phasmid vector pTLPC27, now also called pTIc27 that isdescribed here can be used for the preparation of a phagemid libraryencoding human tear lipocalin muteins. The inventive nucleic acidmolecules coding for the tear lipocalin muteins are inserted into thevector using the two BstXI restriction sites. After ligation a suitablehost strain such as E. coli XL1-Blue is transformed with the resultingnucleic acid mixture to yield a large number of independent clones. Arespective vector can be generated for the preparation of ahyperphagemid library, if desired.

The resulting library is subsequently superinfected in liquid culturewith an appropriate M13-helper phage or hyperphage in order to producefunctional phagemids. The recombinant phagemid displays the lipocalinmutein on its surface as a fusion with the coat protein pIII or afragment thereof, while the N-terminal signal sequence of the fusionprotein is normally cleaved off. On the other hand, it also bears one ormore copies of the native capsid protein pIII supplied by the helperphage and is thus capable of infecting a recipient, in general abacterial strain carrying an F- or F′-plasmid. In case of hyperphagedisplay, the hyperphagemids display the lipocalin muteins on theirsurface as a fusion with the infective coat protein pill but no nativecapsid protein. During or after infection with helper phage orhyperphage, gene expression of the fusion protein between the lipocalinmutein and the capsid protein pIII can be induced, for example byaddition of anhydrotetracycline. The induction conditions are chosensuch that a substantial fraction of the phagemids obtained displays atleast one lipocalin mutein on their surface. In case of hyperphagedisplay induction conditions result in a population of hyperphagemidscarrying between three and five fusion proteins consisting of thelipocalin mutein and the capsid protein pill. Various methods are knownfor isolating the phagemids, such as precipitation with polyethyleneglycol. Isolation typically occurs after an incubation period of 6-8hours.

The isolated phasmids can then be subjected to selection by incubationwith the desired target, wherein the target is presented in a formallowing at least temporary immobilization of those phagemids whichcarry muteins with the desired binding activity as fusion proteins intheir coat. Among the various embodiments known to the person skilled inthe art, the target can, for example, be conjugated with a carrierprotein such as serum albumin and be bound via this carrier protein to aprotein binding surface, for example polystyrene. Microtiter platessuitable for ELISA techniques or so-called “immuno-sticks” can forinstance be used for such an immobilization of the target.Alternatively, conjugates of the target with other binding groups, suchas biotin, can be used. The target can then be immobilized on a surfacewhich selectively binds this group, for example microtiter plates orparamagnetic particles coated with streptavidin, neutravidin or avidin.If the target is fused to an Fc portion of an immunoglobulin,immobilization can also be achieved with surfaces, for examplemicrotiter plates or paramagnetic particles, which are coated withprotein A or protein G.

Non-specific phagemid-binding sites present on the surfaces can besaturated with blocking solutions as they are known for ELISA methods.The phagemids are then typically brought into contact with the targetimmobilized on the surface in the presence of a physiological buffer.Unbound phagemids are removed by multiple washings. The phagemidparticles remaining on the surface are then eluted. For elution, severalmethods are possible. For example, the phagemids can be eluted byaddition of proteases or in the presence of acids, bases, detergents orchaotropic salts or under moderately denaturing conditions. One suchmethod is the elution using buffers of pH 2.2, wherein the eluate issubsequently neutralized. Alternatively, a solution of the free targetcan be added in order to compete with the immobilzed target for bindingto the phagemids or target-specific phagemids can be eluted bycompetition with immunoglobulins or natural liganding proteins whichspecifically bind to the target of interest.

Afterwards, E. coli cells are infected with the eluted phagemids.Alternatively, the nucleic acids can be extracted from the elutedphagemids and used for sequence analysis, amplification ortransformation of cells in another manner. Starting from the E. coliclones obtained in this way, fresh phagemids or hyperphagemids are againproduced by superinfection with M13 helper phages or hyperphageaccording to the method described above and the phagemids amplified inthis way are once again subjected to a selection on the immobilizedtarget. Multiple selection cycles are often necessary in order to obtainthe phagemids with the muteins of the invention in sufficiently enrichedform. The number of selection cycles is in some embodiments chosen insuch a way that in the subsequent functional analysis at least 0.1% ofthe clones studied produce muteins with detectable affinity for thegiven target. Depending on the size, i.e. the complexity of the libraryemployed, 2 to 8 cycles are typically required to this end.

For the functional analysis of the selected muteins, an E. coli strainis infected with the phagemids obtained from the selection cycles andthe corresponding double stranded phasmid DNA is isolated. Starting fromthis phasmid DNA, or also from the single-stranded DNA extracted fromthe phagemids, the nucleic acid sequences of the selected muteins of theinvention can be determined by the methods known in the art and theamino acid sequence can be deduced therefrom. The mutated region or thesequence of the entire tear lipocalin mutein can be subcloned on anotherexpression vector and expressed in a suitable host organism. Forexample, the vector pTLPC26 now also called pTlc26 can be used forexpression in E. coli strains such as E. coli TG1. A muteins of tearlipocalin thus produced can be purified by various biochemical methods.A tear lipocalin mutein produced, for example with pTlc26, may carry anaffinity peptide, a so called affinity tag, for instance at itsC-terminus and can therefore be purified by affinity chromatography.Examples of an affinity tag include, but are not limited to biotin, theStrep-tag, Strep-tag II (Schmidt et al., supra), oligohistidine,polyhistidine, an immunoglobulin domain, maltose-binding protein,glutathione-S-transferase (GST) or calmodulin binding peptide (CBP).

Some affinity tags are haptens, for example but not limited to,dinitrophenol and digoxigenin. Some affinity tags are epitope tags, suchas the FLAG®-peptide (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys-Gly), the T7epitope (Ala-Ser-Met-Thr-GIy-GIy-GIn-Gln-Met-Gly), maltose bindingprotein (MBP), the HSV epitope of the sequenceGIn-Pro-Glu-Leu-Ala-Pro-Glu-Asp-Pro-Glu-Asp of herpes simplex virusglycoprotein D, the hemagglutinin (HA) epitope of the sequenceTyr-Pro-Tyr-Asp-Val-Pro-Asp-Tyr-Ala, the VSV-G epitope of the VesicularStomatitis viral glycoprotein(Cys-Tyr-The-Asp-Ile-Glu-Met-Asn-Arg-Leu-Lys), the E epitope tag of thesequence Gly-Ala-Pro-Val-Pro-Tyr-Pro-Asp-Pro-Leu-Glu-Pro-Arg, the E2epitope tag of the sequenceGly-Val-Ser-Ser-Thr-Ser-Ser-Asp-Phe-Arg-Asp-Arg, the Tag-100 epitope tagof C-termini of mammalian MAPK/ERK kinases of the sequenceGlu-Glu-Thr-Ala-Arg-Phe-Gln-Pro-Gly-Tyr-Arg-Ser, the S-tag of thesequence Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser,the “myc” epitope of the transcription factor c-myc of the sequenceGlu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-Leu and the small V5 epitope presenton the P and V proteins of the paramyxovirus of Simian Virus 5(Gly-Lys-Pro-Ile-Pro-Asn-Pro-Leu-Leu-Gly-Leu-Asp-Ser¬Thr). In addition,but generally not as a single tag, a solubility-enhancing tag such asNusA, thioredoxin (TRX), small ubiquitin-like modifier (SUMO), andubiquitin (Ub) may be used. Haptens and epitope tags may be used incombination with a corresponding antibody or an antibody likeproteinaceous molecule as binding partner. The S-peptide epitope of thesequence Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser maybe used as an epitope tag in connection with a respective antibody or incombination with the S-protein as a binding partner (Hackbarth, J S, etal., BioTechniques (2004) 37, 5, 835-839).

The selection can also be carried out by means of other methods. Manycorresponding embodiments are known to the person skilled in the art orare described in the literature. Moreover, a combination of methods canbe applied. For example, clones selected or at least enriched by “phagedisplay” can additionally be subjected to “colony screening”. Thisprocedure has the advantage that individual clones can directly beisolated with respect to the production of a tear lipocalin mutein withdetectable binding affinity for a target.

In addition to the use of E. coli as host organism in the “phagedisplay” technique or the “colony screening” method, other bacterialstrains, yeast or also insect cells or mammalian cells can be used forthis purpose. Further to the selection of a tear lipocalin mutein from arandom library as described above, evolutive methods including limitedmutagenesis can also be applied in order to optimize a mutein thatalready possesses some binding activity for the target with respect toaffinity or specificity for the target after repeated screening cycles.

It is readily apparent to the skilled person that complex formation isdependent on many factors such as concentration of the binding partners,the presence of competitors, ionic strength of the buffer system etc.Selection and enrichment is generally performed under conditionsallowing the isolation of lipocalin muteins having, in complex with thedesired target, a dissociation constant of at least 200 nM. However, thewashing and elution steps can be carried out under varying stringency. Aselection with respect to the kinetic characteristics is possible aswell. For example, the selection can be performed under conditions,which favor complex formation of the target with muteins that show aslow dissociation from the target, or in other words a low koff rate.Alternatively, selection can be performed under conditions, which favourfast formation of the complex between the mutein and the target, or inother words a high kon rate. As a further illustrative alternative, thescreening can be performed under conditions that select for improvedthermostability of the muteins (compared to either wild type tearlipocalin or a mutein that already has affinity towards a pre-selectedtarget).

Once a mutein with affinity to a given target has been selected, it isadditionally possible to subject such a mutein to another mutagenesis inorder to subsequently select variants of even higher affinity orvariants with improved properties such as higher thermostability,improved serum stability, thermodynamic stability, improved solubility,improved monomeric behavior, improved resistance against thermaldenaturation, chemical denaturation, proteolysis, or detergents etc.This further mutagenesis, which in case of aiming at higher affinity canbe considered as in vitro “affinity maturation”, can be achieved by sitespecific mutation based on rational design or a random mutation. Anotherpossible approach for obtaining a higher affinity or improved propertiesis the use of error-prone PCR, which results in point mutations over aselected range of sequence positions of the lipocalin mutein. Theerror-prone PCR can be carried out in accordance with any known protocolsuch as the one described by Zaccolo et al. (1996) J. Mol. Biol. 255,589-603. Other methods of random mutagenesis that are suitable for suchpurposes include random insertion/deletion (RID) mutagenesis asdescribed by Murakami, H et al. (2002) Nat. Biotechnol. 20, 76-81 ornonhomologous random recombination (NRR) as described by Bittker, J. Aet al. (2002) Nat. Biotechnol. 20, 1024-1029. If desired, affinitymaturation can also be carried out according to the procedure describedin WO 00/75308 or Schlehuber, S. et al., (2000) J. Mol. Biol. 297,1105-1120, where muteins of the bilin-binding protein having highaffinity to digoxigenin were obtained.

A tear lipocalin mutein of the invention may be used for complexformation with IL 4 receptor alpha. The mutein may also be able to bindan immunogenic fragment of IL 4 receptor alpha. An immunogenic fragmentof IL-4 recptor alpha is a fragment that has one or more epitopes,mimotopes or other antigenic determinants, and is thus capable ofinducing an immune response or against which an antibody can be raised.The immunogenic fragment may include a single epitope or may have aplurality of epitopes. Since an antigen-presenting system, e.g. acarrier protein, may be used to provide the size required forrecognition by an immune system, no particular size limitation appliesto the immunogenic fragment. Hence, the immunogenic fragment may also bea “hapten”, i.e. a fragment that need not be antigenic per se or mayhave low immunogenicity, in particular due to its small molecular weightand accordingly size. Typically an immunogenic fragment can, alone orwhen presented on a carrier, be bound by an immunoglobulin or by a Tcell receptor (TCR) if presented by MHC molecules. An immunogenicfragment is typically, alone or when presented in the form of theantigen-presenting system, capable of inducing a humoral immune responseand/or cellular immune response leading for instance to the activationof B- and/or T-lymphocytes.

The target of a mutein of the invention is the alpha chain of theinterleukin-4 receptor, a transmembrane protein, which contains anextracellular domain of 207 amino acids. A secreted form of theextracellular domain exists, sIL-4R alpha, which is also known as CD124and capable of blocking IL-4 activities. A mutein of the invention maybe able to bind sIL-4 receptor alpha as well as any portion of theextracellular domain of IL 4 receptor alpha.

In this context it is also noted that the complex formation between therespective mutein and its ligand is influenced by many different factorssuch as the concentrations of the respective binding partners, thepresence of competitors, pH and the ionic strength of the buffer systemused, and the experimental method used for determination of thedissociation constant K_(D) (for example fluorescence titration,competition ELISA or surface plasmon resonance, just to name a few) oreven the mathematical algorithm which is used for evaluation of theexperimental data.

Therefore, it is also clear to the skilled person that the K_(D) values(dissociation constant of the complex formed between the respectivemutein and its ligand) given here may vary within a certain experimentalrange, depending on the method and experimental setup that is used fordetermining the affinity of a particular lipocalin mutein for a givenligand. This means, there may be a slight deviation in the measuredK_(D) values or a tolerance range depending, for example, on whether theK_(D) value was determined by surface plasmon resonance (Biacore) or bycompetition ELISA.

Also included in the scope of the present invention are forms of theabove muteins, in which the respective mutein has been altered ormodified with respect to its potential immunogenicity.

Cytotoxic T-cells recognize peptide antigens on the cell surface of anantigen-presenting cell in association with a class I majorhistocompatibility complex (MHC) molecule. The ability of the peptidesto bind to MHC molecules is allele specific and correlates with theirimmunogenicity. In order to reduce immunogenicity of a given protein,the ability to predict which peptides in a protein have the potential tobind to a given MHC molecule is of great value. Approaches that employ acomputational threading approach to identify potential T-cell epitopeshave been previously described to predict the binding of a given peptidesequence to MHC class I molecules (Altuvia et al. (1995) J. Mol. Biol.249, 244-250).

Such an approach may also be utilized to identify potential T-cellepitopes in the muteins of the invention and to make depending on itsintended use a selection of a specific mutein on the basis of itspredicted immunogenicity. It may be furthermore possible to subjectpeptide regions which have been predicted to contain T-cell epitopes toadditional mutagenesis to reduce or eliminate these T-cell epitopes andthus minimize immunogenicity. The removal of amphipathic epitopes fromgenetically engineered antibodies has been described (Mateo et al.(2000) Hybridoma 19, 6, 463-471) and may be adapted to the muteins ofthe present invention.

The muteins thus obtained may possess a minimized immunogenicity, whichis desirable for their use in therapeutic and diagnostic applications,such as those described below.

For some applications, it is also useful to employ the muteins of theinvention in a labeled form. Accordingly, the invention is also directedto lipocalin muteins which are conjugated to a label selected from thegroup consisting of enzyme labels, radioactive labels, colored labels,fluorescent labels, chromogenic labels, luminescent labels, haptens,digoxigenin, biotin, metal complexes, metals, and colloidal gold. Themutein may also be conjugated to a low molecular weight organiccompound. The term “low molecular weight organic compound” as usedherein denotes a monomeric carbon-based compound, which may havealiphatic, alicyclic and/or aromatic moieties. In typical embodimentsthe low molecular weight organic compound is an organic compound thathas a main chain of at least two carbon atoms, and in some embodimentsnot more than 7 or 12 rotatable carbon bonds. Such a compound has amolecular weight in the range from about 100 to about 2000 Dalton, suchas from about 100 to about 1000 Dalton. It may optionally include one ortwo metal atoms.

In general, it is possible to label the lipocalin mutein with anyappropriate chemical substance or enzyme, which directly or indirectlygenerates a detectable compound or signal in a chemical, physical,optical, or enzymatic reaction. An example for a physical reaction andat the same time optical reaction/marker is the emission of fluorescenceupon irradiation or the emission of X-rays when using a radioactivelabel. Alkaline phosphatase, horseradish peroxidase or 13-galactosidaseare examples of enzyme labels (and at the same time optical labels)which catalyze the formation of chromogenic reaction products. Ingeneral, all labels commonly used for antibodies (except thoseexclusively used with the sugar moiety in the Fc part ofimmunoglobulins) can also be used for conjugation to the muteins of thepresent invention. The muteins of the invention may also be conjugatedwith any suitable therapeutically active agent, e.g., for the targeteddelivery of such agents to a given cell, tissue or organ or for theselective targeting of cells, e.g., of tumor cells without affecting thesurrounding normal cells. Examples of such therapeutically active agentsinclude radionuclides, toxins, small organic molecules, and therapeuticpeptides (such as peptides acting as agonists/antagonists of a cellsurface receptor or peptides competing for a protein binding site on agiven cellular target). The lipocalin muteins of the invention may,however, also be conjugated with therapeutically active nucleic acidssuch as antisense nucleic acid molecules, small interfering RNAs, microRNAs or ribozymes. Such conjugates can be produced by methods well knownin the art.

In one embodiment, the muteins of the invention may also be coupled to atargeting moiety that targets a specific body region in order to deliverthe inventive muteins to a desired region or area within the body. Oneexample wherein such modification may be desirable is the crossing ofthe blood-brain-barrier. In order to cross the blood-brain barrier, themuteins of the invention may be coupled to moieties that facilitate theactive transport across this barrier (see Gaillard P J, et al.,Diphtheria-toxin receptor-targeted brain drug delivery. InternationalCongress Series, 2005 1277, 185-198 or Gaillard P J, et al. Targeteddelivery across the blood-brain barrier. Expert Opin Drug Deliv. 2005 2,2, 299-309. Such moieties are for example available under the trade name2B-Trans™ (to-BBB technologies BV, Leiden, NL).

As indicated above, a mutein of the invention may in some embodiments beconjugated to a moiety that extends the serum half-life of the mutein(in this regard see also PCT publication WO 2006/56464 where suchconjugation strategies are described with references to muteins of humanneutrophile gelatinase-associated lipocalin with binding affinity forCTLA-4). The moiety that extends the serum half-life may be apolyalkylene glycol molecule, hydroxyethyl starch, fatty acid molecules,such as palmitic acid (Vajo & Duckworth 2000, Pharmacol. Rev. 52, 1-9),an Fc part of an immunoglobulin, a CH3 domain of an immunoglobulin, aCH4 domain of an immunoglobulin, albumin or a fragment thereof, analbumin binding peptide, or an albumin binding protein, transferrin toname only a few. The albumin binding protein may be a bacterial albuminbinding protein, an antibody, an antibody fragment including domainantibodies (see U.S. Pat. No. 6,696,245, for example), or a lipocalinmutein with binding activity for albumin. Accordingly, suitableconjugation partners for extending the half-life of a lipocalin muteinof the invention include albumin (Osborn, B. L. et al., 2002, J.Pharmacol. Exp. Ther. 303, 540-548), or an albumin binding protein, forexample, a bacterial albumin binding domain, such as the one ofstreptococcal protein G (Konig, T., & Skerra, A. (1998) J. Immunol.Methods 218, 73-83). Other examples of albumin binding peptides that canbe used as conjugation partner are, for instance, those having aCys-Xaa1-Xaa2-Xaa3-Xaa4-Cys consensus sequence, wherein Xaa1 is Asp,Asn, Ser, Thr, or Trp; Xaa2 is Asn, Gln, His, Ile, Leu, or Lys; Xaa3 isAla, Asp, Phe, Trp, or Tyr; and Xaa4 is Asp, Gly, Leu, Phe, Ser, or Thras described in US patent application 2003/0069395 or Dennis et al.(Dennis, M. S., Zhang, M., Meng, Y. G., Kadkhodayan, M., Kirchhofer, D.,Combs, D. & Damico, L. A. (2002) J Biol Chem 277, 35035-35043).

In other embodiments, albumin itself or a biological active fragment ofalbumin can be used as conjugation partner of a lipocalin mutein of theinvention. The term “albumin” includes all mammal albumins such as humanserum albumin or bovine serum albumin or rat albumine. The albumin orfragment thereof can be recombinantly produced as described in U.S. Pat.No. 5,728,553 or European patent applications EP 0 330 451 and EP 0 361991. Recombinant human albumin (Recombumin®) Novozymes Delta Ltd.(Nottingham, UK) can be conjugated or fused to a lipocalin mutein inorder to extend the half-life of the mutein.

If the albumin-binding protein is an antibody fragment it may be adomain antibody. Domain Antibodies (dAbs) are engineered to allowprecise control over biophysical properties and in vivo half-life tocreate the optimal safety and efficacy product profile. DomainAntibodies are for example commercially available from Domantis Ltd.(Cambridge, UK and MA, USA).

Using transferrin as a moiety to extend the serum half-life of themuteins of the invention, the muteins can be genetically fused to the Nor C terminus, or both, of non-glycosylated transferrin.Non-glycosylated transferrin has a half-life of 14-17 days, and atransferrin fusion protein will similarly have an extended half-life.The transferrin carrier also provides high bioavailability,biodistribution and circulating stability. This technology iscommercially available from BioRexis (BioRexis PharmaceuticalCorporation, PA, USA). Recombinant human transferrin (DeltaFerrin™) foruse as a protein stabilizer/half-life extension partner is alsocommercially available from Novozymes Delta Ltd. (Nottingham, UK).

If an Fc part of an immunoglobulin is used for the purpose to prolongthe serum half-life of the muteins of the invention, the SynFusion™technology, commercially available from Syntonix Pharmaceuticals, Inc(MA, USA), may be used. The use of this Fc-fusion technology allows thecreation of longer-acting biopharmaceuticals and may for example consistof two copies of the mutein linked to the Fc region of an antibody toimprove pharmacokinetics, solubility, and production efficiency.

Yet another alternative to prolong the half-life of a mutein of theinvention is to fuse to the N- or C-terminus of a mutein of theinvention long, unstructured, flexible glycine-rich sequences (forexample poly-glycine with about 20 to 80 consecutive glycine residues).This approach disclosed in WO2007/038619, for example, has also beenterm “rPEG” (recombinant PEG).

If polyalkylene glycol is used as conjugation partner, the polyalkyleneglycol can be substituted, unsubstituted, linear or branched. It canalso be an activated polyalkylene derivative. Examples of suitablecompounds are polyethylene glycol (PEG) molecules as described in WO99/64016, in U.S. Pat. No. 6,177,074 or in U.S. Pat. No. 6,403,564 inrelation to interferon, or as described for other proteins such asPEG-modified asparaginase, PEG-adenosine deaminase (PEG-ADA) orPEG-superoxide dismutase (see for example, Fuertges et al. (1990) TheClinical Efficacy of Poly(Ethylene Glycol)-Modified Proteins J. Control.Release 11, 139-148). The molecular weight of such a polymer, such aspolyethylene glycol, may range from about 300 to about 70.000 Dalton,including, for example, polyethylene glycol with a molecular weight ofabout 10.000, of about 20.000, of about 30.000 or of about 40.000Dalton. Moreover, as e.g. described in U.S. Pat. No. 6,500,930 or6,620,413, carbohydrate oligo- and polymers such as starch orhydroxyethyl starch (HES) can be conjugated to a mutein of the inventionfor the purpose of serum half-life extension.

If one of the above moieties is conjugated to the human tear lipocalinmutein of the invention, conjugation to an amino acid side chain can beadvantageous. Suitable amino acid side chains may occur naturally in theamino acid sequence of human tear lipocalin or may be introduced bymutagenesis. In case a suitable binding site is introduced viamutagenesis, one possibility is the replacement of an amino acid at theappropriate position by a cysteine residue. In one embodiment, suchmutation includes at least one of Thr 40→Cys, Glu 73→Cys, Arg 90→Cys,Asp 95→Cys or Glu 131→Cys substitution. The newly created cysteineresidue at any of these positions can in the following be utilized toconjugate the mutein to moiety prolonging the serum half-life of themutein, such as PEG or an activated derivative thereof.

In another embodiment, in order to provide suitable amino acid sidechains for conjugating one of the above moieties to the muteins of theinvention artificial amino acids may be introduced by mutagenesis.Generally, such artificial amino acids are designed to be more reactiveand thus to facilitate the conjugation to the desired moiety. Oneexample of such an artificial amino acid that may be introduced via anartificial tRNA is para-acetyl-phenylalanine.

For several applications of the muteins disclosed herein it may beadvantageous to use them in the form of fusion proteins. In someembodiments, the inventive human tear lipocalin mutein is fused at itsN-terminus or its C-terminus to a protein, a protein domain or a peptidesuch as a signal sequence and/or an affinity tag.

For pharmaceutical applications a mutein of the invention may be fusedto a fusion partner that extends the in vivo serum half-life of themutein (see again PCT publication WO 2006/56464 where suitable fusionpartner are described with references to muteins of human neutrophilegelatinase-associated lipocalin with binding affinity for CTLA-4).Similar to the conjugates described above, the fusion partner may be anFc part of an immunoglobulin, a CH3 domain of an immunoglobulin, a CH4domain of an immunoglubolin, albumin, an albumin binding peptide or analbumin binding protein, to name only a few. Again, the albumin bindingprotein may be a bacterial albumin binding protein or a lipocalin muteinwith binding activity for albumin. Accordingly, suitable fusion partnersfor extending the half-life of a lipocalin mutein of the inventioninclude albumin (Osborn, B. L. et al. (2002) supra J. Pharmacol. Exp.Ther. 303, 540-548), or an albumin binding protein, for example, abacterial albumin binding domain, such as the one of streptococcalprotein G (Konig, T., & Skerra, A. (1998) J. Immunol. Methods 218,73-83). The albumin binding peptides described in Dennis et al, supra(2002) or US patent application 2003/0069395 having aCys-Xaa1-Xaa2-Xaa3-Xaa4-Cys consensus sequence, wherein Xaa1 is Asp,Asn, Ser, Thr, or Trp; Xaa2 is Asn, Gn, His, Ile, Leu, or Lys; Xaa3 isAla, Asp, Phe, Trp, or Tyr; and Xaa4 is Asp, Gly, Leu, Phe, Ser, or Thrcan also be used as fusion partner. It is also possible to use albuminitself or a biological active fragment of albumin as fusion partner of alipocalin mutein of the invention. The term “albumin” includes allmammal albumins such as human serum albumin or bovine serum albumin orrat serum albumin. The recombinant production of albumin or fragmentsthereof is well known in the art and for example described in U.S. Pat.No. 5,728,553, European patent application EP 0 330 451 or EP 0 361991.

The fusion partner may confer new characteristics to the inventivelipocalin mutein such as enzymatic activity or binding affinity forother molecules. Examples of suitable fusion proteins are alkalinephosphatase, horseradish peroxidase, gluthation-S-transferase, thealbumin-binding domain of protein G, protein A, antibody fragments,oligomerization domains, lipocalin muteins of same or different bindingspecificity (which results in the formation of “Duocalins”, cf.Schlehuber, S., and Skerra, A. (2001), Duocalins, engineeredligand-binding proteins with dual specificity derived from the lipocalinfold.Bio/. Chem. 382, 1335-1342) or toxins.

In particular, it may be possible to fuse a lipocalin mutein of theinvention with a separate enzyme active site such that both “components”of the resulting fusion protein together act on a given therapeutictarget. The binding domain of the lipocalin mutein attaches to thedisease-causing target, allowing the enzyme domain to abolish thebiological function of the target.

Affinity tags such as the Strep-tag® or Strep-tag® II (Schmidt, T. G. M.et al (1996) J. Mol. Biol. 255, 753-766), the myc-tag, the FLAG-tag®,the His6-tag® or the HA-tag or proteins such asglutathione-S-transferase also allow easy detection and/or purificationof recombinant proteins are further examples of suitable fusionpartners. Finally, proteins with chromogenic or fluorescent propertiessuch as the green fluorescent protein (GFP®) or the yellow fluorescentprotein (YFP) are suitable fusion partners for a lipocalin mutein of theinvention as well.

The term “fusion protein” as used herein also includes lipocalin muteinsaccording to the invention containing a signal sequence. Signalsequences at the N-terminus of a polypeptide direct this polypeptide toa specific cellular compartment, for example the periplasm of E. coli orthe endoplasmatic reticulum of eukaryotic cells. A large number ofsignal sequences is known in the art. An illustrative signal sequencefor secretion a polypeptide into the periplasm of E. coli is theOmpA-signal sequence.

The present invention also relates to nucleic acid molecules (DNA andRNA) that include nucleotide sequences coding for muteins as describedherein. Since the degeneracy of the genetic code permits substitutionsof certain codons by other codons specifying the same amino acid, theinvention is not limited to a specific nucleic acid molecule encoding amutein of the invention but encompasses all nucleic acid molecules thatinclude nucleotide sequences encoding a functional mutein.

Therefore, the present invention also includes a nucleic acid sequenceencoding a mutein according to the invention that has a mutation at atleast one codon of any of the amino acid sequence positions 26-34,56-58, 80, 83, 104-106 and 108 of the linear polypeptide sequence ofnative mature human tear lipocalin, wherein the codons encoding at leastone of the cysteine residues at sequence positions 61 and 153 of thelinear polypeptide sequence of the mature human tear lipocalin have beenmutated to encode any other amino acid residue.

The invention as disclosed herein also includes nucleic acid moleculesencoding tear lipocalin muteins, which include additional mutationsoutside the indicated sequence positions of experimental mutagenesis.Such mutations are often tolerated or can even prove to be advantageous,for example if they contribute to an improved folding efficiency, serumstability, thermal stability or ligand binding affinity of the mutein.

A nucleic acid molecule disclosed in this application may be “operablylinked” to a regulatory sequence (or regulatory sequences) to allowexpression of this nucleic acid molecule.

A nucleic acid molecule, such as DNA, is referred to as “capable ofexpressing a nucleic acid molecule” or capable “to allow expression of anucleotide sequence” if it includes sequence elements which containinformation regarding to transcriptional and/or translationalregulation, and such sequences are “operably linked” to the nucleotidesequence encoding the polypeptide. An operable linkage is a linkage inwhich the regulatory sequence elements and the sequence to be expressedare connected in a way that enables gene expression. The precise natureof the regulatory regions necessary for gene expression may vary amongspecies, but in general these regions include a promoter which, inprokaryotes, contains both the promoter per se, i.e. DNA elementsdirecting the initiation of transcription, as well as DNA elementswhich, when transcribed into RNA, will signal the initiation oftranslation. Such promoter regions normally include 5′ non-codingsequences involved in initiation of transcription and translation, suchas the −35/−10 boxes and the Shine-Dalgarno element in prokaryotes orthe TATA box, CAAT sequences, and 5′-capping elements in eukaryotes.These regions can also include enhancer or repressor elements as well astranslated signal and leader sequences for targeting the nativepolypeptide to a specific compartment of a host cell.

In addition, the 3′ non-coding sequences may contain regulatory elementsinvolved in transcriptional termination, polyadenylation or the like.If, however, these termination sequences are not satisfactory functionalin a particular host cell, then they may be substituted with signalsfunctional in that cell.

Therefore, a nucleic acid molecule of the invention can include aregulatory sequence, such as a promoter sequence. In some embodiments anucleic acid molecule of the invention includes a promoter sequence anda transcriptional termination sequence. Suitable prokaryotic promotersare, for example, the tet promoter, the lacUV5 promoter or the T7promoter. Examples of promoters useful for expression in eukaryoticcells are the SV40 promoter or the CMV promoter.

The nucleic acid molecules of the invention can also be part of a vectoror any other kind of cloning vehicle, such as a plasmid, a phagemid, aphage, a baculovirus, a cosmid or an artificial chromosome.

In one embodiment, the nucleic acid molecule is included in a phasmid. Aphasmid vector denotes a vector encoding the intergenic region of atemperent phage, such as M13 or f1, or a functional part thereof fusedto the cDNA of interest. After superinfection of the bacterial hostcells with such an phagemid vector and an appropriate helper phage (e.g.M13K07, VCS-M13 or R408) intact phage particles are produced, therebyenabling physical coupling of the encoded heterologous cDNA to itscorresponding polypeptide displayed on the phage surface (see e.g.Lowman, H. B. (1997) Annu. Rev. Biophys. Biomol. Struct. 26, 401-424, orRodi, D. J., and Makowski, L. (1999) Curr. Opin. Biotechnol. 10, 87-93).

Such cloning vehicles can include, aside from the regulatory sequencesdescribed above and a nucleic acid sequence encoding a lipocalin muteinof the invention, replication and control sequences derived from aspecies compatible with the host cell that is used for expression aswell as selection markers conferring a selectable phenotype ontransformed or transfected cells. Large numbers of suitable cloningvectors are known in the art, and are commercially available.

The DNA molecule encoding lipocalin muteins of the invention, and inparticular a cloning vector containing the coding sequence of such alipocalin mutein can be transformed into a host cell capable ofexpressing the gene. Transformation can be performed using standardtechniques. Thus, the invention is also directed to a host cellcontaining a nucleic acid molecule as disclosed herein.

The transformed host cells are cultured under conditions suitable forexpression of the nucleotide sequence encoding a fusion protein of theinvention. Suitable host cells can be prokaryotic, such as Escherichiacoli (E. coli) or Bacillus subtilis, or eukaryotic, such asSaccharomyces cerevisiae, Pichia pastoris, SF9 or High5 insect cells,immortalized mammalian cell lines (e.g. HeLa cells or CHO cells) orprimary mammalian cells.

The invention also relates to a method for the production of a mutein ofthe invention, wherein the mutein, a fragment of the mutein or a fusionprotein of the mutein and another polypeptide is produced starting fromthe nucleic acid coding for the mutein by means of genetic engineeringmethods. The method can be carried out in vivo, the mutein can forexample be produced in a bacterial or eucaryotic host organism and thenisolated from this host organism or its culture. It is also possible toproduce a protein in vitro, for example by use of an in vitrotranslation system.

When producing the mutein in vivo a nucleic acid encoding a mutein ofthe invention is introduced into a suitable bacterial or eukaryotic hostorganism by means of recombinant DNA technology (as already outlinedabove). For this purpose, the host cell is first transformed with acloning vector that includes a nucleic acid molecule encoding a muteinof the invention using established standard methods. The host cell isthen cultured under conditions, which allow expression of theheterologous DNA and thus the synthesis of the correspondingpolypeptide. Subsequently, the polypeptide is recovered either from thecell or from the cultivation medium.

In some tear lipocalin muteins of the invention, the naturally occurringdisulfide bond between Cys 61 and Cys 153 is removed. Accordingly, suchmuteins (or any other tear lipocalin mutein that does not include anintramolecular disulfide bond) can be produced in a cell compartmenthaving a reducing redox milieu, for example, in the cytoplasma ofGram-negative bacteria. In case a lipocalin mutein of the inventionincludes intramolecular disulfide bonds, it may be desired to direct thenascent polypeptide to a cell compartment having an oxidizing redoxmilieu using an appropriate signal sequence. Such an oxidizingenvironment may be provided by the periplasm of Gram-negative bacteriasuch as E. coli, in the extracellular milieu of Gram-positive bacteriaor in the lumen of the endoplasmatic reticulum of eukaryotic cells andusually favors the formation of structural disulfide bonds. It is,however, also possible to produce a mutein of the invention in thecytosol of a host cell, such as E. coli. In this case, the polypeptidecan either be directly obtained in a soluble and folded state orrecovered in form of inclusion bodies, followed by renaturation invitro. A further option is the use of specific host strains having anoxidizing intracellular milieu, which may thus allow the formation ofdisulfide bonds in the cytosol (Venturi M, et al. (2002) J. Mol. Biol.315, 1-8).

However, a mutein of the invention may not necessarily be generated orproduced only by use of genetic engineering. Rather, a lipocalin muteincan also be obtained by chemical synthesis such as Merrifield solidphase polypeptide synthesis or by in vitro transcription andtranslation. It is for example possible that promising mutations areidentified using molecular modeling and then to synthesize the wanted(designed) polypeptide in vitro and investigate the binding activity fora given target. Methods for the solid phase and/or solution phasesynthesis of proteins are well known in the art (see e.g. Bruckdorfer,T. et al. (2004) Curr. Pharm. Biotechnol. 5, 29-43).

In another embodiment, the muteins of the invention may be produced byin vitro transcription/translation employing well-established methodsknown to those skilled in the art.

The invention also relates to a pharmaceutical composition, whichincludes at least one inventive mutein of human tear lipocalin or afusion protein or conjugate thereof and a pharmaceutically acceptableexcipient.

The lipocalin muteins according to the invention can be administered viaany parenteral or non-parenteral (enteral) route that is therapeuticallyeffective for proteinaceous drugs. The muteins of the invention can beadministered systemically or topically in formulations containingconventional non-toxic pharmaceutically acceptable excipients orcarriers, additives and vehicles as desired.

In one embodiment of the present invention the pharmaceutical isadministered parenterally to a mammal, and in particular to humans. Thepharmaceutical composition may be an aqueous solution, an oil-in wateremulsion or a water-in-oil emulsion.

In this regard it is noted that transdermal delivery technologies, e.g.iontophoresis, sonophoresis or microneedle-enhanced delivery, asdescribed in Meidan V M and Michniak B B (2004) Am. J. Ther. 11, 4,312-316, can also be used for transdermal delivery of the muteinsdescribed herein. The muteins of the invention can be administeredsystemically or topically in formulations containing a variety ofconventional non-toxic pharmaceutically acceptable excipients orcarriers, additives, and vehicles.

The dosage of the mutein applied may vary within wide limits to achievethe desired preventive effect or therapeutic response. It will, forinstance, depend on the affinity of the compound for a chosen ligand aswell as on the half-life of the complex between the mutein and theligand in vivo. Further, the optimal dosage will depend on thebiodistribution of the mutein or its fusion protein or its conjugate,the mode of administration, the severity of the disease/disorder beingtreated as well as the medical condition of the patient. For example,when used in an ointment for topical applications, a high concentrationof the tear lipocalin mutein can be used. However, if wanted, the muteinmay also be given in a sustained release formulation, for exampleliposomal dispersions or hydrogel-based polymer microspheres, likePolyActive™ or OctoDEX™ (Polymers for controlled release, cf. Bos etal., Business Briefing: Pharmatech 2003, 1-6). Other sustained releaseformulations available are for example PLGA based polymers (PRpharmaceuticals), PLA-PEG based hydrogels (Medincell®) and PEA basedpolymers (Medivas®).

Accordingly, the muteins of the present invention can be formulated intocompositions using pharmaceutically acceptable ingredients as well asestablished methods of preparation. The pharmaceutical composition mayalso contain additives, such as, for example, fillers, binders, wettingagents, glidants, stabilizers, preservatives, emulsifiers, andfurthermore solvents or solubilizers or agents for achieving a depoteffect. The latter is that fusion proteins may be incorporated into slowor sustained release or targeted delivery systems, such as liposomes andmicrocapsules.

The formulations can be sterilized by numerous means, includingfiltration through a bacteria-retaining filter, or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile medium justprior to use.

A lipocalin mutein described herein can be administered to an organism,including a human patient per se, or in a pharmaceutical compositionwhere it may include or be mixed with pharmaceutically activeingredients or suitable carriers or excipient(s). Techniques forformulation and administration of a respective lipocalin muteincomposition resemble or are identical to those of low molecular weightcompounds well established in the art. Exemplary routes include, but arenot limited to, oral, transdermal, and parenteral delivery.

A composition that includes a lipocalin mutein of the invention may forinstance be applied onto the skin or onto a wound. In some embodimentsone may administer a lipocalin mutein or a respective composition in alocal rather than systemic manner, for example, via injection.

Pharmaceutical compositions that include a lipocalin mutein of thepresent invention may be manufactured in a manner that is itself known,e. g., by means of conventional mixing, dissolving, granulating,dragee-making, levigating, emulsifying, encapsulating, entrapping orlyophilizing processes. A pharmaceutical composition for use inaccordance with the present invention thus may be formulated inconventional manner using one or more physiologically acceptablecarriers including excipients and auxiliaries that facilitate processingof the hydrogel and/or peptide/peptoid into preparations that can beused pharmaceutically. Proper formulation is dependent upon the route ofadministration chosen.

For injection, the lipocalin mutein or a respective composition may beformulated in aqueous solutions, for instance in physiologicallycompatible buffers such as Hanks's solution, Ringer's solution, orphysiological saline buffer. For transmucosal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art.

For oral administration, the lipocalin mutein or a respectivecomposition can be formulated readily by combining them withpharmaceutically acceptable carriers well known in the art. Suchcarriers enable the lipocalin mutein or a respective composition, aswell as a pharmaceutically active compound where present, to beformulated as tablets, pills, dragees, capsules, liquids, gels, syrups,slurries, suspensions and the like, for oral ingestion by a patient tobe treated. Pharmaceutical preparations for oral use can be obtained byadding a solid excipient, optionally grinding a resulting mixture, andprocessing the mixture of granules, after adding suitable auxiliaries,if desired, to obtain tablets or dragee cores. Suitable excipients are,in particular, fillers such as sugars, including lactose, sucrose,mannitol, or sorbitol; cellulose preparations such as, for example,maize starch, wheat starch, rice starch, potato starch, gelatine, gumtragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodiumcarboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired,disintegrating agents may be added, such as the cross-linked polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodiumalginate.

Dragee cores are provided with suitable coatings. For this purpose,concentrated sugar solutions may be used, which may optionally containgum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethyleneglycol, and/or titanium dioxide, lacquer solutions, and suitable organicsolvents or solvent mixtures. Dyestuffs or pigments may be added to thetablets or dragee coatings for identification or to characterizedifferent combinations of active compound doses.

Pharmaceutical preparations that can be used orally include push-fitcapsules made of gelatine, as well as soft, sealed capsules made ofgelatine and a plasticizer, such as glycerol or sorbitol. The push-fitcapsules can contain the active ingredients in admixture with fillersuch as lactose, binders such as starches, and/or lubricants such astalc or magnesium stearate and, optionally, stabilizers. In softcapsules, the peptides/peptoids may be suspended in suitable liquids,such as fatty oils, liquid paraffin, or liquid polyethylene glycols. Inaddition, stabilizers may be added. All formulations for oraladministration should be in dosages suitable for such administration.

The lipocalin mutein may be formulated for parenteral administration byinjection, e.g., by intramuscular injections or bolus injection orcontinuous infusion. Formulations for injection may be presented in unitdosage form, e. g., in ampules or in multi-dose containers, with anadded preservative. The respective compositions may take such forms assuspensions, solutions or emulsions in oily or aqueous vehicles, and maycontain formulatory agents such as suspending, stabilizing and/ordispersing agents.

The subject in need of such a treatment may be a mammal, such as ahuman, a dog, a mouse, a rat, a pig, an ape such as cymologous to nameonly a few illustrative examples. A mutein of the present invention canbe used to treat any disease or disorder that involves IL-4 receptoralpha, in the development of such disease or disorder can be displayedto the expression product of a nucleic acid library of the presentinvention or displayed to otherwise obtained muteins of tear lipocalin.

In this context it is noted that a variety of tumor cells express agreater number of high affinity IL-4 receptors than normal cells. Suchcells include solid human tumor such as melanoma, breast cancer, ovariancarcinoma, mesothelioma, glioblastoma, astrocytoma, renal cellcarcinoma, head and neck carcinoma, AIDS associated Kaposi'ssarcoma=AIDS KS, hormone dependent and independent prostate carcinomacells, and primary cultures from prostate tumors, for example (cf.Garland, L, et al., (2005) Journal of Immunotherapy 28, 4, 376-381,Rand, R W, et al. Clinical Cancer Research. (2000) 6, 2157-2165; HusainS R, et al. (1999) Nature Medicine 5, 817-822; Puri R K, et al. CancerResearch (1996) 56, 5631-5637; Debinski W, et al, or Husain S R, et al.Cancer Research (1998) 58, 3649-3653, Kawakami K, et al. (2000) CancerResearch, 60, 2981-2987; or Strome S E, et al. Clinical Cancer Research(2002) 8, 281-286, for example. Specific examples of cells withdocuments overexpression of IL-4 receptors include, but are not limitedto, Burkitt lymphoma cell line Jijoye (B-cell lymphom), prostatecarcinoma (LNCaP, DU145), head and neck carcinoma (SCC, KCCT873),Pranceatic cancer (PANC-1 cell line), SCC-25: 13.000 (+/−500) h head andneck cancer cell line (ATCC). IL4R alpha chain plays a major role inIL4-internalization. Accordingly, when fused or conjugated to a toxin,the tear lipocalin muteins binding to IL-4 Receptor alpha chain cantherefore also be used for the treatment of tumors (cancer). Examples ofsuitable toxins include Pseudomonas exotoxin, pertussis-toxin,diphtheria toxin, ricin, saporin, pseudomonas exotoxin, calicheamicin ora derivative thereof, a taxoid, a maytansinoid, a tubulysin and adolastatin analogue. Examples of dolastatin analogues include, but arenot limited to, auristatin E, monomethylauristatin E, auristatin PYE andauristatin PHE.

For the treatment of cancer, it is also possible to conjugate muteinsbinding to IL-4 Receptor alpha chain to a cystostatic agent. Examples ofsuch cystostatic agents include Cisplatin, Carboplatin, Oxaliplatin,5-Fluorouracil, Taxotere (Docetaxel), Paclitaxel, Anthracycline(Doxorubicin), Methotrexate, Vinblastin, Vincristine, Vindesine,Vinorelbine, Dacarbazine, Cyclophosphamide, Etoposide, Adriamycine,Camptotecine, Combretatastin A-4 related compounds, sulfonamides,oxadiazolines, benzo[b]thiophenessynthetic spiroketal pyrans,monotetrahydrofuran compounds, curacin and curacin derivatives,methoxyestradiol derivatives and Leucovorin.

As is evident from the above disclosure, a mutein of the presentinvention or a fusion protein or a conjugate thereof can be employed inmany applications. In general, such a mutein can be used in allapplications antibodies are used, except those with specifically rely onthe glycosylation of the Fc part.

Therefore, in another aspect of the invention, the invented muteins ofhuman tear lipocalin are used for the detection of a given non-naturalligand of human tear lipocalin. Such use may include the steps ofcontacting the mutein with a sample suspected of containing the givenligand under suitable conditions, thereby allowing formation of acomplex between the mutein and the given ligand, and detecting thecomplexed mutein by a suitable signal.

The detectable signal can be caused by a label, as explained above, orby a change of physical properties due to the binding, i.e. the complexformation, itself. One example is plasmon surface resonance, the valueof which is changed during binding of binding partners from which one isimmobilized on a surface such as a gold foil.

The muteins of human tear lipocalin disclosed herein may also be usedfor the separation of a given non-natural ligand of human tearlipocalin. Such use may include the steps of contacting the mutein witha sample supposed to contain said ligand under suitable conditions,thereby allowing formation of a complex between the mutein and the givenligand, and separating the mutein/ligand complex from the sample.

In both the use of the mutein for the detection of a given non-naturalligand as well as the separation of a given ligand, the mutein and/orthe target may be immobilized on a suitable solid phase.

The human tear lipocalin muteins of the invention may also be used totarget a compound to a preselected site. For such a purpose the muteinis contacted with the compound of interest in order to allow complexformation. Then the complex that includes the mutein and the compound ofinterest are delivered to the preselected site. This use is inparticular suitable, but not restricted to, for delivering a drug(selectively) to a preselected site in an organism, such as an infectedbody part, tissue or organ which is supposed to be treated with thedrug. Besides formation of a complex between mutein and compound ofinterest, the mutein can also be reacted with the given compound toyield a conjugate of mutein and compound. Similar to the above complex,such a conjugate may be suitable to deliver the compound to thepreselected target site. Such a conjugate of mutein and compound mayalso include a linker that covalently links mutein and compound to eachother. Optionally, such a linker is stable in the bloodstream but iscleavable in a cellular environment.

The muteins disclosed herein and its derivatives can thus be used inmany fields similar to antibodies or fragments thereof. In addition totheir use for binding to a support, allowing the target of a givenmutein or a conjugate or a fusion protein of this target to beimmobilized or separated, the muteins can be used for labeling with anenzyme, an antibody, a radioactive substance or any other group havingbiochemical activity or defined binding characteristics. By doing so,their respective targets or conjugates or fusion proteins thereof can bedetected or brought in contact with them. For example, muteins of theinvention can serve to detect chemical structures by means ofestablished analytical methods (e.g. ELISA or Western Blot) or bymicroscopy or immunosensorics. Here, the detection signal can either begenerated directly by use of a suitable mutein conjugate or fusionprotein or indirectly by immunochemical detection of the bound muteinvia an antibody.

Numerous possible applications for the inventive muteins also exist inmedicine. In addition to their use in diagnostics and drug delivery, amutant polypeptide of the invention, which binds, for example, tissue-or tumor-specific cellular surface molecules can be generated. Such amutein may, for example, be employed in conjugated form or as a fusionprotein for “tumor imaging” or directly for cancer therapy. Accordingly,the present invention provides a diagnostic composition comprising aninventive mutein and means for diagnosis such as excipients, buffers,labels (which can be used to label the muteins).

Thus, the present invention also involves the use of the human tearlipocalin muteins of the invention for complex formation with a givennon-natural ligand.

Another related use of a mutein described herein is target validation,i.e. the analysis whether a polypeptide assumed to be involved in thedevelopment or progress of a disease or disorder is indeed somehowcausative of that disease or disorder. This use for validating a proteinas a pharmacological drug target takes advantage of the ability of amutein of the present invention to specifically recognize a surface areaof a protein in its native conformation, i.e. to bind to a nativeepitope. In this respect, it is to be noted that this ability has beenreported only for a limited number of recombinant antibodies. However,the use of an inventive mutein for validation of a drug target is notlimited to the detection of proteins as targets, but also includes thedetection of protein domains, peptides, nucleic acid molecules, organicmolecules or metal complexes.

EXEMPLARY EMBODIMENT OF THE INVENTION

FIG. 1 shows the primary structure of a previously disclosed human tearlipocalin mutein (S191.4-B24) that exhibits binding affinity for IL-4receptor alpha. The first 21 residues (underlined) constitute the signalsequence, which is cleaved upon periplasmic expression. The N-terminalT7-tag (italic) and the C-terminal Streptag-II (bold) are part of thecharacterized protein. FIG. 1 also shows that 4 N-terminal amino acidresidues (His1 His2 Leu3 Ala4) as well as the two last C-terminal aminoacid residues (Ser157 and Asp158) of the wild type tear lipocalin aredeleted in this mutein.

FIGS. 2A-2F show the polypeptide sequences of exemplary muteins withhigh affinity for IL-4 receptor alpha (SEQ ID Nos: 2-11). Numbersindicated by ‘SwissProt P31025’ show the corresponding amino acidposition numbering of the unprocessed precursor sequence of the entry ofthe SwissProt database. Wt TLc26 essentially corresponds to the sequenceof wild type tear lipocalin in the vector pTLc26. However, wt TLc26 doesnot include a disulfide bond, since the cystein residues at positions 61and 153 of the mature protein are replaced by serine residues. Likewise,a serine residue at positions 101 of the mature protein is replaced by aserine residue. In addition, at position 111 of the mature protein anarginine residue has been replaced by a proline and at position 114 ofthe mature protein a lysine residue has been replaced by a tryptophan.Furthermore, the two C-terminal amino acids included in the sequence ofSwissProt entry P31025 are not included in the sequence. AB4004 is arandomization library disclosed in international patent application WO2008/015239, in which the mutated positions are indicated in bold.Randomized sequences are identical to J14 with the exception of position53 and 55. M3-B24(PSM) indicates hot spots from PSM B24.

FIGS. 3A-3B show the results of TF-1 cell proliferation assays. TF-1cells were incubated for 1 hour at 37° C. with the indicated muteins ofthe invention (S276.2 K04, S308.5 F08, S308.5 N01, S308.5 L20, S308.5L04, S308.5 N20, S308.3 010, S191.4 B24 [SEQ ID Nos: 2-11]) in adilution series before addition of 0.8 ng/ml IL-4 (A) or 12 ng/ml IL-13(B) for 72 h. Proliferation was measured by 3H-thymidine incorporation.

FIG. 4 depicts IC50 values from FIG. 3 and results of Biacore®measurements of the muteins of human tear lipocalin with affinity forIL-4 receptor alpha. Approximately 400 RU of IL-4 receptor alpha-Fc wascaptured on a CM-5 chip, which had previously been coated with an antihuman-Fc monoclonal antibody. Subsequently, mutein in a singleconcentration of 25 nM was passed over the flowcell and changes inresonance units recorded. Reference signals from a flow cell that wasequally treated apart from not having any IL-4 receptor alpha-Fc wassubtracted and the resulting data fitted to a 1:1 Langmuir model usingthe BIAevaluation software. Due to the slow dissociation kinetics of thedouble referencing was used by subtracting the signals from a flow cellthat was equally treated apart from not having any IL-4 receptoralpha-Fc and subtracting the signal from an experiment where only samplebuffer was injected. The resulting data was fitted to a 1:1 Langmuirmodel with mass-transport limitation using the BIAevaluation software.

Unless otherwise indicated, established methods in the art ofrecombinant gene technology were used.

EXAMPLES Example 1: Affinity Maturation of the Mutein S91.4-B24 Using aSite-Directed Random Approach

A library of variants based on the mutein S191.4-B24 (SEQ ID NO:2) thatis described in PCT application WO 2008/015239 was designed byrandomization of the positions 26, 32, 34, 55, 56, 58 and 63 to allowfor all 20 amino acids on these positions. The library was constructedessentially as described in Example 1 of WO 2008/015239.

Phagemid selection was carried out as described in Example 2 of WO2008/015239 using limited target concentration (0.5 nM and 0.1 nM ofIL-4 receptor alpha, Peprotech) combined with extended washing timestogether with a competitive monoclonal antibody against IL-4 receptoralpha (MAB230, R&D Systems; 1 hour washing) or short incubation times(10 minutes), respectively. Three or four rounds of selection wereperformed.

Preparative production of IL4 receptor alpha-specific muteins wascarried out using E. coli K12 strain JM83 harbouring the respectivemutein encoded on the expression vector pTLPC10 (SEQ ID No: 1) or, wherelarger amounts of protein were needed, E. coli strain W3110 harbouringthe respective expression vector as described in WO 2008/015239.

Example 2: Affinity Measurement Using Biacore®

Affinity measurements were performed essentially as described in Example9 of WO 2006/56464 with the modifications that approximately 400 RU ofIL-4 receptor alpha-Fc (R&D Systems) was immobilized (instead of 2000 RUof human CTLA-4 or murine CTLA-4-Fc used as target in WO 2006/56464) and100 μl of mutein was injected at a concentration of 25 nM (instead of 40μl sample purified lipocalin muteins at concentrations of 5-0.3 pM asused in WO 2006/56464).

Example 3: TF-1 Cell Proliferation Assays

IL-4 and IL-13-stimulated TF-1 cell proliferation assays were performedessentially as described in Lefort et al (Lefort S., et al., (1995) FEBSLett. 366, 2-3, 122-126) and as described in Example 10 of PCTapplication WO 2008/015239. TF-1 cells were incubated for 1 hour at 37°C. with the indicated muteins muteins of the invention (S276.2 K04,S308.5 F08, S308.5 NO1, S308.5 L20, S308.5 L04, S308.5 N20, S308.3 010,S191.4 B24 [SEQ ID Nos: 3-11]) in a dilution series before addition of0.8 ng/ml IL-4 (a) or 12 ng/ml IL-13 (b) for 72 h. Proliferation wasmeasured by 3H-thymidine incorporation. The results from a TF-1proliferation assay is depicted in Figure and shows that the highaffinity variants S276.2 K04, S308.5 F08, S308.5 N01, S308.5 L20, S308.5L04, S308.5 N20, and S308.3O10 are potent antagonists of IL-4 as well asIL-13 induced signalling and proliferation.

One skilled in the art would readily appreciate that the presentinvention is well adapted to carry out the objects and obtain the endsand advantages mentioned, as well as those inherent therein. Further, itwill be readily apparent to one skilled in the art that varyingsubstitutions and modifications may be made to the invention disclosedherein without departing from the scope and spirit of the invention. Thecompositions, methods, procedures, treatments, molecules and specificcompounds described herein are presently representative of certainembodiments are exemplary and are not intended as limitations on thescope of the invention. Changes therein and other uses will occur tothose skilled in the art which are encompassed within the spirit of theinvention are defined by the scope of the claims. The listing ordiscussion of a previously published document in this specificationshould not necessarily be taken as an acknowledgement that the documentis part of the state of the art or is common general knowledge.

The invention illustratively described herein may suitably be practicedin the absence of any element or elements, limitation or limitations,not specifically disclosed herein. Thus, for example, the terms“comprising”, “including,” containing”, etc. shall be read expansivelyand without limitation. Additionally, the terms and expressions employedherein have been used as terms of description and not of limitation, andthere is no intention in the use of such terms and expressions ofexcluding any equivalents of the features shown and described orportions thereof, but it is recognized that various modifications arepossible within the scope of the invention claimed. Thus, it should beunderstood that although the present invention has been specificallydisclosed by exemplary embodiments and optional features, modificationand variation of the inventions embodied therein herein disclosed may beresorted to by those skilled in the art, and that such modifications andvariations are considered to be within the scope of this invention.

The invention has been described broadly and generically herein. Each ofthe narrower species and subgeneric groupings falling within the genericdisclosure also form part of the invention. This includes the genericdescription of the invention with a proviso or negative limitationremoving any subject matter from the genus, regardless of whether or notthe excised material is specifically recited herein.

Other embodiments are within the following claims. In addition, wherefeatures or aspects of the invention are described in terms of Markushgroups, those skilled in the art will recognize that the invention isalso thereby described in terms of any individual member or subgroup ofmembers of the Markush group.

1-19. (canceled)
 20. A mutein of human tear lipocalin, wherein the aminoacid sequence of the mutein comprises: A SDEEI QDVSG TWYLK AMTVD SRCPRAVYNS VTPMT LTTLE GGNLE AKFTA QRKGR WQKYK LVLEK TDEPG KYTAS GGRHV AYIIRSHVKD HYIFH SEGLC PGQPV PGVWL VGRDP KNNLE ALEDF EKAAG ARGLS TESIL IPRQSETSSP G.
 21. A method of generating a mutein of human tear lipocalin ofclaim 20, wherein the mutein binds to IL-4 receptor alpha, comprising:(a) subjecting a nucleic acid molecule encoding a human tear lipocalinto mutagenesis at the amino acid sequence positions 27, 28, 30, 31, 33,53, 57, 61, 64, 66, 80, 83, 104-106 and 108 of the linear polypeptidesequence of mature human tear lipocalin, and further, subjecting thenucleic acid molecule encoding a human tear lipocalin to mutagenesis atthe amino acid sequence positions 26, 32, 34, 55, 56, 58 and 63 of thelinear polypeptide sequence of mature human tear lipocalin, (b)expressing one or more nucleic acid molecule(s) obtained in step (a) inan expression system, thereby obtaining one or more mutein(s) and (c)enriching the one or more mutein(s) obtained in step (b) that bind tohuman IL-4 receptor alpha by means of selection and/or isolation. 22.The method of claim 21, wherein step (c) comprises: (ci) providing IL-4receptor alpha or an immunogenic fragment thereof, (cii) contacting theone or more mutein(s) with the IL-4 receptor alpha or the immunogenicfragment thereof, thereby allowing the formation of a complex betweenthe IL-4 receptor alpha or the immunogenic fragment thereof and a muteinhaving binding affinity for the same, and (ciii) removing mutein(s)having no or no substantial binding affinity.
 23. The method of claim21, wherein the selection in step (c) is carried out under competitiveconditions.
 24. A nucleic acid molecule comprising a nucleotide sequenceencoding a mutein of claim
 20. 25. A host cell containing a nucleic acidmolecule of claim
 24. 26. A pharmaceutical composition comprising amutein of human tear lipocalin as defined in claim 20 and apharmaceutically acceptable excipient.